MARQ 0.0.1

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  1. data/LICENSE +20 -0
  2. data/R/CustomDS.R +80 -0
  3. data/R/GEO.R +249 -0
  4. data/R/MA.R +359 -0
  5. data/README.rdoc +29 -0
  6. data/bin/marq_config +170 -0
  7. data/install_scripts/CustomDS/Rakefile +223 -0
  8. data/install_scripts/GEO/Rakefile +258 -0
  9. data/install_scripts/GEO/platforms/GPL100.yaml +7 -0
  10. data/install_scripts/GEO/platforms/GPL1002.yaml +7 -0
  11. data/install_scripts/GEO/platforms/GPL1007.yaml +7 -0
  12. data/install_scripts/GEO/platforms/GPL101.yaml +7 -0
  13. data/install_scripts/GEO/platforms/GPL1010.yaml +7 -0
  14. data/install_scripts/GEO/platforms/GPL1073.yaml +7 -0
  15. data/install_scripts/GEO/platforms/GPL1074.yaml +4 -0
  16. data/install_scripts/GEO/platforms/GPL1090.yaml +7 -0
  17. data/install_scripts/GEO/platforms/GPL1104.yaml +7 -0
  18. data/install_scripts/GEO/platforms/GPL118.yaml +7 -0
  19. data/install_scripts/GEO/platforms/GPL1205.yaml +4 -0
  20. data/install_scripts/GEO/platforms/GPL1211.yaml +7 -0
  21. data/install_scripts/GEO/platforms/GPL1213.yaml +7 -0
  22. data/install_scripts/GEO/platforms/GPL1219.yaml +4 -0
  23. data/install_scripts/GEO/platforms/GPL1223.yaml +7 -0
  24. data/install_scripts/GEO/platforms/GPL1226.yaml +7 -0
  25. data/install_scripts/GEO/platforms/GPL1229.yaml +7 -0
  26. data/install_scripts/GEO/platforms/GPL1230.yaml +7 -0
  27. data/install_scripts/GEO/platforms/GPL1231.yaml +7 -0
  28. data/install_scripts/GEO/platforms/GPL1232.yaml +7 -0
  29. data/install_scripts/GEO/platforms/GPL1260.yaml +4 -0
  30. data/install_scripts/GEO/platforms/GPL1261.yaml +4 -0
  31. data/install_scripts/GEO/platforms/GPL127.yaml +4 -0
  32. data/install_scripts/GEO/platforms/GPL128.yaml +7 -0
  33. data/install_scripts/GEO/platforms/GPL1290.yaml +7 -0
  34. data/install_scripts/GEO/platforms/GPL1292.yaml +7 -0
  35. data/install_scripts/GEO/platforms/GPL1293.yaml +7 -0
  36. data/install_scripts/GEO/platforms/GPL1294.yaml +7 -0
  37. data/install_scripts/GEO/platforms/GPL1295.yaml +7 -0
  38. data/install_scripts/GEO/platforms/GPL13.yaml +4 -0
  39. data/install_scripts/GEO/platforms/GPL1310.yaml +7 -0
  40. data/install_scripts/GEO/platforms/GPL1313.yaml +7 -0
  41. data/install_scripts/GEO/platforms/GPL1323.yaml +7 -0
  42. data/install_scripts/GEO/platforms/GPL1331.yaml +7 -0
  43. data/install_scripts/GEO/platforms/GPL1352.yaml +4 -0
  44. data/install_scripts/GEO/platforms/GPL1355.yaml +4 -0
  45. data/install_scripts/GEO/platforms/GPL1382.yaml +7 -0
  46. data/install_scripts/GEO/platforms/GPL1387.yaml +7 -0
  47. data/install_scripts/GEO/platforms/GPL1397.yaml +4 -0
  48. data/install_scripts/GEO/platforms/GPL14.yaml +7 -0
  49. data/install_scripts/GEO/platforms/GPL1412.yaml +7 -0
  50. data/install_scripts/GEO/platforms/GPL1415.yaml +7 -0
  51. data/install_scripts/GEO/platforms/GPL1420.yaml +7 -0
  52. data/install_scripts/GEO/platforms/GPL144.yaml +7 -0
  53. data/install_scripts/GEO/platforms/GPL1449.yaml +7 -0
  54. data/install_scripts/GEO/platforms/GPL1458.yaml +7 -0
  55. data/install_scripts/GEO/platforms/GPL1523.yaml +7 -0
  56. data/install_scripts/GEO/platforms/GPL1524.yaml +7 -0
  57. data/install_scripts/GEO/platforms/GPL1528.yaml +7 -0
  58. data/install_scripts/GEO/platforms/GPL153.yaml +7 -0
  59. data/install_scripts/GEO/platforms/GPL1530.yaml +7 -0
  60. data/install_scripts/GEO/platforms/GPL1535.yaml +4 -0
  61. data/install_scripts/GEO/platforms/GPL155.yaml +7 -0
  62. data/install_scripts/GEO/platforms/GPL163.yaml +7 -0
  63. data/install_scripts/GEO/platforms/GPL168.yaml +7 -0
  64. data/install_scripts/GEO/platforms/GPL169.yaml +7 -0
  65. data/install_scripts/GEO/platforms/GPL1704.yaml +4 -0
  66. data/install_scripts/GEO/platforms/GPL1708.yaml +7 -0
  67. data/install_scripts/GEO/platforms/GPL1739.yaml +7 -0
  68. data/install_scripts/GEO/platforms/GPL1740.yaml +4 -0
  69. data/install_scripts/GEO/platforms/GPL1749.yaml +7 -0
  70. data/install_scripts/GEO/platforms/GPL177.yaml +7 -0
  71. data/install_scripts/GEO/platforms/GPL1790.yaml +7 -0
  72. data/install_scripts/GEO/platforms/GPL1792.yaml +7 -0
  73. data/install_scripts/GEO/platforms/GPL181.yaml +7 -0
  74. data/install_scripts/GEO/platforms/GPL1818.yaml +7 -0
  75. data/install_scripts/GEO/platforms/GPL1820.yaml +4 -0
  76. data/install_scripts/GEO/platforms/GPL1823.yaml +7 -0
  77. data/install_scripts/GEO/platforms/GPL1826.yaml +7 -0
  78. data/install_scripts/GEO/platforms/GPL183.yaml +7 -0
  79. data/install_scripts/GEO/platforms/GPL1831.yaml +7 -0
  80. data/install_scripts/GEO/platforms/GPL1833.yaml +7 -0
  81. data/install_scripts/GEO/platforms/GPL1872.yaml +4 -0
  82. data/install_scripts/GEO/platforms/GPL1911.yaml +7 -0
  83. data/install_scripts/GEO/platforms/GPL1914.yaml +4 -0
  84. data/install_scripts/GEO/platforms/GPL1928.yaml +7 -0
  85. data/install_scripts/GEO/platforms/GPL1942.yaml +7 -0
  86. data/install_scripts/GEO/platforms/GPL1945.yaml +7 -0
  87. data/install_scripts/GEO/platforms/GPL1964.yaml +7 -0
  88. data/install_scripts/GEO/platforms/GPL198.yaml +4 -0
  89. data/install_scripts/GEO/platforms/GPL1981.yaml +4 -0
  90. data/install_scripts/GEO/platforms/GPL200.yaml +7 -0
  91. data/install_scripts/GEO/platforms/GPL2006.yaml +7 -0
  92. data/install_scripts/GEO/platforms/GPL201.yaml +4 -0
  93. data/install_scripts/GEO/platforms/GPL2011.yaml +7 -0
  94. data/install_scripts/GEO/platforms/GPL2026.yaml +7 -0
  95. data/install_scripts/GEO/platforms/GPL205.yaml +7 -0
  96. data/install_scripts/GEO/platforms/GPL207.yaml +7 -0
  97. data/install_scripts/GEO/platforms/GPL2136.yaml +7 -0
  98. data/install_scripts/GEO/platforms/GPL220.yaml +7 -0
  99. data/install_scripts/GEO/platforms/GPL226.yaml +7 -0
  100. data/install_scripts/GEO/platforms/GPL24.yaml +4 -0
  101. data/install_scripts/GEO/platforms/GPL246.yaml +4 -0
  102. data/install_scripts/GEO/platforms/GPL247.yaml +7 -0
  103. data/install_scripts/GEO/platforms/GPL2507.yaml +4 -0
  104. data/install_scripts/GEO/platforms/GPL2529.yaml +4 -0
  105. data/install_scripts/GEO/platforms/GPL2531.yaml +7 -0
  106. data/install_scripts/GEO/platforms/GPL254.yaml +7 -0
  107. data/install_scripts/GEO/platforms/GPL2569.yaml +7 -0
  108. data/install_scripts/GEO/platforms/GPL257.yaml +7 -0
  109. data/install_scripts/GEO/platforms/GPL2598.yaml +7 -0
  110. data/install_scripts/GEO/platforms/GPL260.yaml +7 -0
  111. data/install_scripts/GEO/platforms/GPL2614.yaml +4 -0
  112. data/install_scripts/GEO/platforms/GPL2622.yaml +7 -0
  113. data/install_scripts/GEO/platforms/GPL2623.yaml +7 -0
  114. data/install_scripts/GEO/platforms/GPL2660.yaml +7 -0
  115. data/install_scripts/GEO/platforms/GPL2670.yaml +7 -0
  116. data/install_scripts/GEO/platforms/GPL2677.yaml +7 -0
  117. data/install_scripts/GEO/platforms/GPL2700.yaml +4 -0
  118. data/install_scripts/GEO/platforms/GPL2721.yaml +7 -0
  119. data/install_scripts/GEO/platforms/GPL2727.yaml +7 -0
  120. data/install_scripts/GEO/platforms/GPL273.yaml +7 -0
  121. data/install_scripts/GEO/platforms/GPL2763.yaml +7 -0
  122. data/install_scripts/GEO/platforms/GPL2824.yaml +7 -0
  123. data/install_scripts/GEO/platforms/GPL284.yaml +7 -0
  124. data/install_scripts/GEO/platforms/GPL287.yaml +4 -0
  125. data/install_scripts/GEO/platforms/GPL2872.yaml +7 -0
  126. data/install_scripts/GEO/platforms/GPL288.yaml +4 -0
  127. data/install_scripts/GEO/platforms/GPL2883.yaml +7 -0
  128. data/install_scripts/GEO/platforms/GPL289.yaml +4 -0
  129. data/install_scripts/GEO/platforms/GPL2895.yaml +4 -0
  130. data/install_scripts/GEO/platforms/GPL2897.yaml +7 -0
  131. data/install_scripts/GEO/platforms/GPL2902.yaml +7 -0
  132. data/install_scripts/GEO/platforms/GPL2987.yaml +4 -0
  133. data/install_scripts/GEO/platforms/GPL2995.yaml +7 -0
  134. data/install_scripts/GEO/platforms/GPL3039.yaml +4 -0
  135. data/install_scripts/GEO/platforms/GPL3050.yaml +7 -0
  136. data/install_scripts/GEO/platforms/GPL3084.yaml +7 -0
  137. data/install_scripts/GEO/platforms/GPL3113.yaml +7 -0
  138. data/install_scripts/GEO/platforms/GPL317.yaml +7 -0
  139. data/install_scripts/GEO/platforms/GPL319.yaml +7 -0
  140. data/install_scripts/GEO/platforms/GPL32.yaml +4 -0
  141. data/install_scripts/GEO/platforms/GPL3222.yaml +7 -0
  142. data/install_scripts/GEO/platforms/GPL3295.yaml +7 -0
  143. data/install_scripts/GEO/platforms/GPL3305.yaml +4 -0
  144. data/install_scripts/GEO/platforms/GPL3306.yaml +7 -0
  145. data/install_scripts/GEO/platforms/GPL3307.yaml +7 -0
  146. data/install_scripts/GEO/platforms/GPL333.yaml +4 -0
  147. data/install_scripts/GEO/platforms/GPL3341.yaml +7 -0
  148. data/install_scripts/GEO/platforms/GPL3349.yaml +7 -0
  149. data/install_scripts/GEO/platforms/GPL339.yaml +4 -0
  150. data/install_scripts/GEO/platforms/GPL340.yaml +4 -0
  151. data/install_scripts/GEO/platforms/GPL3408.yaml +7 -0
  152. data/install_scripts/GEO/platforms/GPL341.yaml +4 -0
  153. data/install_scripts/GEO/platforms/GPL3415.yaml +4 -0
  154. data/install_scripts/GEO/platforms/GPL3423.yaml +7 -0
  155. data/install_scripts/GEO/platforms/GPL3440.yaml +7 -0
  156. data/install_scripts/GEO/platforms/GPL3457.yaml +4 -0
  157. data/install_scripts/GEO/platforms/GPL3504.yaml +4 -0
  158. data/install_scripts/GEO/platforms/GPL3506.yaml +4 -0
  159. data/install_scripts/GEO/platforms/GPL355.yaml +7 -0
  160. data/install_scripts/GEO/platforms/GPL3558.yaml +7 -0
  161. data/install_scripts/GEO/platforms/GPL3607.yaml +7 -0
  162. data/install_scripts/GEO/platforms/GPL368.yaml +4 -0
  163. data/install_scripts/GEO/platforms/GPL3695.yaml +7 -0
  164. data/install_scripts/GEO/platforms/GPL371.yaml +7 -0
  165. data/install_scripts/GEO/platforms/GPL3834.yaml +4 -0
  166. data/install_scripts/GEO/platforms/GPL4006.yaml +7 -0
  167. data/install_scripts/GEO/platforms/GPL4055.yaml +7 -0
  168. data/install_scripts/GEO/platforms/GPL409.yaml +7 -0
  169. data/install_scripts/GEO/platforms/GPL4191.yaml +7 -0
  170. data/install_scripts/GEO/platforms/GPL4226.yaml +7 -0
  171. data/install_scripts/GEO/platforms/GPL4371.yaml +7 -0
  172. data/install_scripts/GEO/platforms/GPL4567.yaml +4 -0
  173. data/install_scripts/GEO/platforms/GPL4685.yaml +4 -0
  174. data/install_scripts/GEO/platforms/GPL483.yaml +7 -0
  175. data/install_scripts/GEO/platforms/GPL49.yaml +7 -0
  176. data/install_scripts/GEO/platforms/GPL50.yaml +7 -0
  177. data/install_scripts/GEO/platforms/GPL500.yaml +7 -0
  178. data/install_scripts/GEO/platforms/GPL507.yaml +4 -0
  179. data/install_scripts/GEO/platforms/GPL51.yaml +7 -0
  180. data/install_scripts/GEO/platforms/GPL513.yaml +7 -0
  181. data/install_scripts/GEO/platforms/GPL519.yaml +7 -0
  182. data/install_scripts/GEO/platforms/GPL52.yaml +7 -0
  183. data/install_scripts/GEO/platforms/GPL529.yaml +7 -0
  184. data/install_scripts/GEO/platforms/GPL53.yaml +7 -0
  185. data/install_scripts/GEO/platforms/GPL5356.yaml +7 -0
  186. data/install_scripts/GEO/platforms/GPL538.yaml +7 -0
  187. data/install_scripts/GEO/platforms/GPL54.yaml +7 -0
  188. data/install_scripts/GEO/platforms/GPL543.yaml +7 -0
  189. data/install_scripts/GEO/platforms/GPL544.yaml +7 -0
  190. data/install_scripts/GEO/platforms/GPL545.yaml +7 -0
  191. data/install_scripts/GEO/platforms/GPL546.yaml +7 -0
  192. data/install_scripts/GEO/platforms/GPL547.yaml +7 -0
  193. data/install_scripts/GEO/platforms/GPL549.yaml +7 -0
  194. data/install_scripts/GEO/platforms/GPL550.yaml +4 -0
  195. data/install_scripts/GEO/platforms/GPL56.yaml +7 -0
  196. data/install_scripts/GEO/platforms/GPL560.yaml +4 -0
  197. data/install_scripts/GEO/platforms/GPL564.yaml +7 -0
  198. data/install_scripts/GEO/platforms/GPL57.yaml +7 -0
  199. data/install_scripts/GEO/platforms/GPL570.yaml +4 -0
  200. data/install_scripts/GEO/platforms/GPL571.yaml +4 -0
  201. data/install_scripts/GEO/platforms/GPL576.yaml +7 -0
  202. data/install_scripts/GEO/platforms/GPL58.yaml +7 -0
  203. data/install_scripts/GEO/platforms/GPL5823.yaml +4 -0
  204. data/install_scripts/GEO/platforms/GPL59.yaml +7 -0
  205. data/install_scripts/GEO/platforms/GPL5915.yaml +4 -0
  206. data/install_scripts/GEO/platforms/GPL5947.yaml +7 -0
  207. data/install_scripts/GEO/platforms/GPL61.yaml +7 -0
  208. data/install_scripts/GEO/platforms/GPL64.yaml +7 -0
  209. data/install_scripts/GEO/platforms/GPL6419.yaml +7 -0
  210. data/install_scripts/GEO/platforms/GPL6424.yaml +7 -0
  211. data/install_scripts/GEO/platforms/GPL65.yaml +7 -0
  212. data/install_scripts/GEO/platforms/GPL6574.yaml +4 -0
  213. data/install_scripts/GEO/platforms/GPL6649.yaml +4 -0
  214. data/install_scripts/GEO/platforms/GPL67.yaml +7 -0
  215. data/install_scripts/GEO/platforms/GPL6720.yaml +7 -0
  216. data/install_scripts/GEO/platforms/GPL7054.yaml +4 -0
  217. data/install_scripts/GEO/platforms/GPL737.yaml +7 -0
  218. data/install_scripts/GEO/platforms/GPL738.yaml +7 -0
  219. data/install_scripts/GEO/platforms/GPL74.yaml +4 -0
  220. data/install_scripts/GEO/platforms/GPL75.yaml +4 -0
  221. data/install_scripts/GEO/platforms/GPL76.yaml +4 -0
  222. data/install_scripts/GEO/platforms/GPL764.yaml +7 -0
  223. data/install_scripts/GEO/platforms/GPL772.yaml +7 -0
  224. data/install_scripts/GEO/platforms/GPL782.yaml +7 -0
  225. data/install_scripts/GEO/platforms/GPL783.yaml +7 -0
  226. data/install_scripts/GEO/platforms/GPL784.yaml +7 -0
  227. data/install_scripts/GEO/platforms/GPL80.yaml +4 -0
  228. data/install_scripts/GEO/platforms/GPL81.yaml +4 -0
  229. data/install_scripts/GEO/platforms/GPL82.yaml +4 -0
  230. data/install_scripts/GEO/platforms/GPL83.yaml +4 -0
  231. data/install_scripts/GEO/platforms/GPL85.yaml +4 -0
  232. data/install_scripts/GEO/platforms/GPL86.yaml +4 -0
  233. data/install_scripts/GEO/platforms/GPL87.yaml +4 -0
  234. data/install_scripts/GEO/platforms/GPL870.yaml +7 -0
  235. data/install_scripts/GEO/platforms/GPL875.yaml +7 -0
  236. data/install_scripts/GEO/platforms/GPL884.yaml +7 -0
  237. data/install_scripts/GEO/platforms/GPL887.yaml +7 -0
  238. data/install_scripts/GEO/platforms/GPL89.yaml +4 -0
  239. data/install_scripts/GEO/platforms/GPL890.yaml +7 -0
  240. data/install_scripts/GEO/platforms/GPL891.yaml +7 -0
  241. data/install_scripts/GEO/platforms/GPL90.yaml +7 -0
  242. data/install_scripts/GEO/platforms/GPL91.yaml +4 -0
  243. data/install_scripts/GEO/platforms/GPL92.yaml +4 -0
  244. data/install_scripts/GEO/platforms/GPL920.yaml +7 -0
  245. data/install_scripts/GEO/platforms/GPL922.yaml +7 -0
  246. data/install_scripts/GEO/platforms/GPL924.yaml +7 -0
  247. data/install_scripts/GEO/platforms/GPL93.yaml +4 -0
  248. data/install_scripts/GEO/platforms/GPL96.yaml +4 -0
  249. data/install_scripts/GEO/platforms/GPL968.yaml +4 -0
  250. data/install_scripts/GEO/platforms/GPL97.yaml +4 -0
  251. data/install_scripts/GEO/platforms/GPL98.yaml +7 -0
  252. data/install_scripts/GEO/platforms/GPL981.yaml +7 -0
  253. data/install_scripts/GEO/platforms/GPL99.yaml +7 -0
  254. data/install_scripts/GEO/platforms/GPL999.yaml +7 -0
  255. data/install_scripts/GEO/series/GSE10018.yaml +61 -0
  256. data/install_scripts/GEO/series/GSE1002.yaml +135 -0
  257. data/install_scripts/GEO/series/GSE10066.yaml +31 -0
  258. data/install_scripts/GEO/series/GSE10073.yaml +19 -0
  259. data/install_scripts/GEO/series/GSE10091.yaml +15 -0
  260. data/install_scripts/GEO/series/GSE101.yaml +17 -0
  261. data/install_scripts/GEO/series/GSE10100.yaml +15 -0
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  267. data/install_scripts/GEO/series/GSE103.yaml +19 -0
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  270. data/install_scripts/GEO/series/GSE10521.yaml +56 -0
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  272. data/install_scripts/GEO/series/GSE1073.yaml +127 -0
  273. data/install_scripts/GEO/series/GSE10860.yaml +25 -0
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  300. data/install_scripts/GEO/series/GSE12104.yaml +10 -0
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  302. data/install_scripts/GEO/series/GSE12150.yaml +32 -0
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  305. data/install_scripts/GEO/series/GSE1365.yaml +14 -0
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  307. data/install_scripts/GEO/series/GSE1492.yaml +15 -0
  308. data/install_scripts/GEO/series/GSE15222.yaml +731 -0
  309. data/install_scripts/GEO/series/GSE1553.yaml +23 -0
  310. data/install_scripts/GEO/series/GSE1617.yaml +39 -0
  311. data/install_scripts/GEO/series/GSE1688.yaml +36 -0
  312. data/install_scripts/GEO/series/GSE1693.yaml +60 -0
  313. data/install_scripts/GEO/series/GSE1752.yaml +32 -0
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@@ -0,0 +1,23 @@
1
+ = light_color_link(!light_font_color)
2
+ :color= !light_font_color
3
+ &:visited, &:link
4
+ :color= !light_font_color
5
+ :text-decoration none
6
+ &:hover
7
+ :color red
8
+ :text-decoration none
9
+
10
+ = button(!background_color, !hover_color, !hover_background_color, !round_corner_radius= 5)
11
+ +round-corners(!round_corner_radius)
12
+ :color black
13
+ :text-decoration none
14
+ :text-align center
15
+ :font-weight bold
16
+ :font-size 0.9em
17
+ :background-color= !background_color
18
+ :padding 1px 4px 1px 4px
19
+ &:hover
20
+ :background-color= !hover_background_color
21
+ :color= !hover_color
22
+
23
+
@@ -0,0 +1,35 @@
1
+ // round corners (base)
2
+ = round-corners(!radius = 10)
3
+ -moz-border-radius: #{!radius}px
4
+ -webkit-border-radius: #{!radius}px
5
+ border-radius: #{!radius}px
6
+
7
+ // top rounded corners
8
+ = round-corners-top(!radius = 10)
9
+ +round-corners-top-left(!radius)
10
+ +round-corners-top-right(!radius)
11
+
12
+ = round-corners-top-left(!radius = 10)
13
+ -moz-border-radius-topleft: #{!radius}px
14
+ -webkit-border-top-left-radius: #{!radius}px
15
+ border-top-left-radius: #{!radius}px
16
+
17
+ = round-corners-top-right(!radius = 10)
18
+ -moz-border-radius-topright: #{!radius}px
19
+ -webkit-border-top-right-radius: #{!radius}px
20
+ border-top-right-radius: #{!radius}px
21
+
22
+ // bottom rounded corners
23
+ = round-corners-bottom(!radius = 10)
24
+ +round-corners-bottom-left(!radius)
25
+ +round-corners-bottom-right(!radius)
26
+
27
+ = round-corners-bottom-left(!radius = 10)
28
+ -moz-border-radius-bottomleft: #{!radius}px
29
+ -webkit-border-bottom-left-radius: #{!radius}px
30
+ border-bottom-left-radius: #{!radius}px
31
+
32
+ = round-corners-bottom-right(!radius = 10)
33
+ -moz-border-radius-bottomright: #{!radius}px
34
+ -webkit-border-bottom-right-radius: #{!radius}px
35
+ border-bottom-right-radius: #{!radius}px
@@ -0,0 +1,63 @@
1
+ <div id="container">
2
+ <div id="header-container">
3
+ <img src="/images/merb.jpg" />
4
+ <!-- <h1>Mongrel + Erb</h1> -->
5
+ <h2>pocket rocket web framework</h2>
6
+ <hr />
7
+ </div>
8
+
9
+ <div id="left-container">
10
+ <h3>Exception:</h3>
11
+ <p><%= request.exceptions.first.message %></p>
12
+ </div>
13
+
14
+ <div id="main-container">
15
+ <h3>Why am I seeing this page?</h3>
16
+ <p>Merb couldn't find an appropriate content_type to return,
17
+ based on what you said was available via provides() and
18
+ what the client requested.</p>
19
+
20
+ <h3>How to add a mime-type</h3>
21
+ <pre><code>
22
+ Merb.add_mime_type :pdf, :to_pdf, %w[application/pdf], &quot;Content-Encoding&quot; =&gt; &quot;gzip&quot;
23
+ </code></pre>
24
+ <h3>What this means is:</h3>
25
+ <ul>
26
+ <li>Add a mime-type for :pdf</li>
27
+ <li>Register the method for converting objects to PDF as <code>#to_pdf</code>.</li>
28
+ <li>Register the incoming mime-type "Accept" header as <code>application/pdf</code>.</li>
29
+ <li>Specify a new header for PDF types so it will set <code>Content-Encoding</code> to gzip.</li>
30
+ </ul>
31
+
32
+ <h3>You can then do:</h3>
33
+ <pre><code>
34
+ class Foo &lt; Application
35
+ provides :pdf
36
+ end
37
+ </code></pre>
38
+
39
+ <h3>Where can I find help?</h3>
40
+ <p>If you have any questions or if you can't figure something out, please take a
41
+ look at our <a href="http://merbivore.com/"> project page</a>,
42
+ feel free to come chat at irc.freenode.net, channel #merb,
43
+ or post to <a href="http://groups.google.com/group/merb">merb mailing list</a>
44
+ on Google Groups.</p>
45
+
46
+ <h3>What if I've found a bug?</h3>
47
+ <p>If you want to file a bug or make your own contribution to Merb,
48
+ feel free to register and create a ticket at our
49
+ <a href="http://merb.lighthouseapp.com/">project development page</a>
50
+ on Lighthouse.</p>
51
+
52
+ <h3>How do I edit this page?</h3>
53
+ <p>You can change what people see when this happens by editing <tt>app/views/exceptions/not_acceptable.html.erb</tt>.</p>
54
+
55
+ </div>
56
+
57
+ <div id="footer-container">
58
+ <hr />
59
+ <div class="left"></div>
60
+ <div class="right">&copy; 2008 the merb dev team</div>
61
+ <p>&nbsp;</p>
62
+ </div>
63
+ </div>
@@ -0,0 +1,47 @@
1
+ <div id="container">
2
+ <div id="header-container">
3
+ <img src="/images/merb.jpg" />
4
+ <!-- <h1>Mongrel + Erb</h1> -->
5
+ <h2>pocket rocket web framework</h2>
6
+ <hr />
7
+ </div>
8
+
9
+ <div id="left-container">
10
+ <h3>Exception:</h3>
11
+ <p><%= request.exceptions.first.message %></p>
12
+ </div>
13
+
14
+ <div id="main-container">
15
+ <h3>Welcome to Merb!</h3>
16
+ <p>Merb is a light-weight MVC framework written in Ruby. We hope you enjoy it.</p>
17
+
18
+ <h3>Where can I find help?</h3>
19
+ <p>If you have any questions or if you can't figure something out, please take a
20
+ look at our <a href="http://merbivore.com/"> project page</a>,
21
+ feel free to come chat at irc.freenode.net, channel #merb,
22
+ or post to <a href="http://groups.google.com/group/merb">merb mailing list</a>
23
+ on Google Groups.</p>
24
+
25
+ <h3>What if I've found a bug?</h3>
26
+ <p>If you want to file a bug or make your own contribution to Merb,
27
+ feel free to register and create a ticket at our
28
+ <a href="http://merb.lighthouseapp.com/">project development page</a>
29
+ on Lighthouse.</p>
30
+
31
+ <h3>How do I edit this page?</h3>
32
+ <p>You're seeing this page because you need to edit the following files:
33
+ <ul>
34
+ <li>config/router.rb <strong><em>(recommended)</em></strong></li>
35
+ <li>app/views/exceptions/not_found.html.erb <strong><em>(recommended)</em></strong></li>
36
+ <li>app/views/layout/application.html.erb <strong><em>(change this layout)</em></strong></li>
37
+ </ul>
38
+ </p>
39
+ </div>
40
+
41
+ <div id="footer-container">
42
+ <hr />
43
+ <div class="left"></div>
44
+ <div class="right">&copy; 2008 the merb dev team</div>
45
+ <p>&nbsp;</p>
46
+ </div>
47
+ </div>
@@ -0,0 +1,4 @@
1
+ .menu
2
+ %a{:href => '/help', :class => (selected == 'main' ? 'selected': '')} Overview
3
+ %a{:href => '/help/methods', :class => (selected == 'meth' ? 'selected': '')} Methods
4
+ %a{:href => '/help/quick', :class => (selected == 'quick' ? 'selected': '')} Quick start guide!
@@ -0,0 +1,110 @@
1
+ :javascript
2
+ current = 'help'
3
+ #help
4
+
5
+ = partial 'menu', :selected => 'main'
6
+
7
+ #video
8
+ =partial 'partials/video'
9
+
10
+
11
+ :redcloth
12
+ h1. Introduction
13
+
14
+ MARQ is an online microarray retrieval tool based on rank statistics.
15
+ Datasets in MARQ, most of them retrieved from GEO, are processed into
16
+ signatures, which are lists of genes ranked by their level of differential
17
+ expression. Each dataset defines one of more of these signatures based on
18
+ the possible comparisons of its constituent samples.
19
+
20
+ The user may query MARQ using two lists of genes, one represents
21
+ over-expressed genes and the other under-expressed genes. The gene lists
22
+ are compared against the signatures in MARQ to determine which of those
23
+ signatures have similar or opposite patterns of expression. The result of
24
+ the analysis is the list of signatures sorted by their relevance to the
25
+ query; signatures in the top show the strongest direct relationship
26
+ with the query, and signatures in the bottom show the strongest inverse
27
+ relationship.
28
+
29
+ MARQ offers some additional features to help the user explore the results,
30
+ enabling the user to examine the actual ranks of the query genes in
31
+ a signature or the distribution of terms amongst the list of signatures,
32
+ or even to perform meta-analysis between interesting signatures.
33
+
34
+ Check the "methods":/help/methods for more information about
35
+ implementation details. The "Quick Start Guide":/help/quick and the
36
+ <a href="#TB_inline?height=410&width=640&inlineId=video" title="Quick Start Guide! video" class="thickbox">Video tutorial</a>
37
+ have a more visual introduction to the usage of the web.
38
+
39
+ h1. Usage
40
+
41
+ h2. Launching a job
42
+
43
+ MARQ offers two modes of operation: per-platform, and cross-platform. In
44
+ the first mode, per platform, the user inputs the query genes using the
45
+ same format of a given microarray platform in GEO. The per-platform mode of
46
+ operation only considers signatures in one particular platform, but
47
+ performs the query using all the original probes for that platform. The
48
+ cross-platform considers all the platforms for a given organism, but
49
+ translates both the probes in the datasets and the query genes to a common
50
+ gene Id format. This reduces the number of elements in each signature, as
51
+ different probes are associated to the same gene and some probes can not be
52
+ translated at all.
53
+
54
+ Performing a query entails selecting an organism, the platform to query, or
55
+ that a cross-platform must be performed, and the up and down gene lists. It
56
+ is also possible to specify just one of the up and down regulated gene
57
+ lists and have the other one ignored just by leaving it empty. Note that
58
+ when the two lists are used they both have the same weight in the final
59
+ score, regardless of the number of genes in each one.
60
+
61
+ h2. Results
62
+
63
+ The main page of results shows a table will all the signatures sorted by
64
+ their relationship with the query. The top of the lists shows signatures
65
+ with a direct relationship with the query, while the bottom shows
66
+ signatures with an inverse relationship. The hit-area left of the table
67
+ represents the complete list of signatures, the extremes are differently
68
+ colored indicating datasets with a significant p-value (after FDR
69
+ correction). Double clicking this hit-area will scroll the table to the
70
+ correspondent signature. This hit-area is also used to mark datasets
71
+ sharing annotation terms, as described below.
72
+
73
+ Due to the heuristic criteria used in determining the "order of the
74
+ samples":/help/methods#comparisons in each comparison, signatures may have
75
+ their samples reversed from what would be their logical order, thus
76
+ to be found at one extreme of the list when they should intuitively appear at
77
+ the other. For this reason, it is important to check both the top and bottom
78
+ of the list.
79
+
80
+ For each signature there are images that show the positions of the genes
81
+ from each query list in that signature. Each signature also has a hits page
82
+ for the up and down query lists that shows additional information about the
83
+ genes, like their rank in the signature, their synonyms, and, if the
84
+ dataset is a GEO dataset, a link to the genes profile in GEO. The values
85
+ for the log-ratios and t-values for the genes in the signatures, as
86
+ computed by the MARQ differential expression analysis pipeline, are also
87
+ available for download.
88
+
89
+ Also, each signature contains additional information such the text from the
90
+ title and description of the datasets or GO terms enriched in each
91
+ comparison (see "signature annotations":/help/methods#go_annotations for
92
+ details). This information is used in the annotations tool: Words in the
93
+ text of a dataset description and title may be clicked to mark other
94
+ signatures containing those same words, and similarly for GO based
95
+ annotations. Signatures sharing that particular annotation term are marked
96
+ as lines in the hit-area. Double clicking over one of those lines will
97
+ scroll to the relevant signature. An 'Annotations menu' allows to include
98
+ GO based annotations, which are not processed initially by default like
99
+ word annotations. It also shows which annotation terms are significantly
100
+ represented in the extremes of the signature list. This last functionality
101
+ shares the same scoring function as the actual signature scoring.
102
+
103
+ Finally, two or more signatures may be selected for comparison. This
104
+ consists on a meta-analysis of the common genes to all these signatures
105
+ using "Rank Product":http://www.ncbi.nlm.nih.gov/pubmed/15327980. The main
106
+ assumption of this analysis is that a gene can be considered over-expressed
107
+ if it appears among the most over-expressed for all signatures.
108
+
109
+
110
+
@@ -0,0 +1,301 @@
1
+ :javascript
2
+ current = 'help'
3
+ #methods
4
+
5
+
6
+ =partial 'menu', :selected => 'meth'
7
+
8
+ :redcloth
9
+
10
+ h1. Signature Database generation
11
+
12
+ We use NCBI E-utils to determine all available platforms and datasets for
13
+ each supported organism. Each dataset is loaded into R using the GEOquery
14
+ package and a differential expression analysis is performed using limma.
15
+ Linear data are log transformed. The results from the differential
16
+ expression analysis are used to sort the genes in the dataset to generate
17
+ the signatures. We perform one differential analysis for each of the
18
+ "comparisons":/help/methods#comparisons between samples. If limma succeeds
19
+ in performing the analysis, then the resulting t-values are used to rank
20
+ the genes in the signature. If it fails, due to lack of sample replicates
21
+ for example, we resort to the log ratios.
22
+
23
+ Each dataset is process two times: once using the original data, and once
24
+ after all the probe ids are "translated":/help/methods#translations into
25
+ a common id format.
26
+
27
+ h3(#comparisons). Comparisons
28
+
29
+ Each datasets has one or more features, which represent experimental
30
+ conditions (what is commonly referred to as the phenotype), that group
31
+ samples into classes. For instance, a feature could be the _tissue_, and
32
+ the classes would be _tumor_ or _normal_. For each of the features we
33
+ compare classes one to one. We do not define sub-classes by combining
34
+ classes from different features. If one of the classes is identified as a
35
+ control class, then all other classes are compared against it. If not, all
36
+ classes are compared against each other. The particular order in this last
37
+ case is arbitrary and may result in making some comparison in a different
38
+ order from what would be expected (A vs B or B vs A). At the time of this
39
+ writing, a class is considered a control if it contains one of the
40
+ following terms in its description: @none@, @control@, @normal@, @wild@,
41
+ @baseline@, @untreated@, @uninfected@, @universal@, @reference@, @wt@, or
42
+ @vehicle@.
43
+
44
+
45
+ h1(#score). Signature Comparison
46
+
47
+ Signature comparison consists in assigning a score to a signature based on
48
+ the positions of the query genes. The signature been the list of genes
49
+ ranked by differential expression in the corresponding comparison. The
50
+ query genes are divided in two lists, up-regulated genes and down-regulated
51
+ genes. Each of the two lists receives a score, the final score is the
52
+ combination of the scores for both lists. We may call each of these scores
53
+ !/images/meth/S_up.gif! for the up-regulated list and
54
+ !/images/meth/S_down.gif! for the down-regulated list. Each of these two
55
+ scores is calculated using the following procedure:
56
+
57
+ * Let !/images/meth/Q.gif! be the set of !/images/meth/q.gif! genes in the
58
+ correspondent query list (up-regulated or down-regulated). Let
59
+ !/images/meth/G.gif! be the list of !/images/meth/g.gif! genes in the
60
+ signature sorted by their differential expression value (t-value or log-ratio).
61
+ Consider in !/images/meth/Q.gif! only those genes appearing in the
62
+ signature list !/images/meth/G.gif!, the rest are considered missing, let
63
+ !/images/meth/m.gif! be the number of such missing genes.
64
+
65
+
66
+ * Genes at the top or bottom extremes of the signature are the most
67
+ up-regulated and down-regulated respectively, and their contribution is
68
+ weighted higher in the score. Genes receive a weight that is a function of
69
+ their position in the signature. We define !/images/meth/d.gif! as the
70
+ distance of gene !/images/meth/i.gif! to the center of the signature scaled
71
+ to be !/images/meth/d_range.gif!: !(large)/images/meth/d_formula.gif!.
72
+ Where !/images/meth/p.gif! is the position in the signature.
73
+ The distances !/images/meth/d.gif! are used to compute the weights for each
74
+ gene !/images/meth/w.gif! using a "weight function":#weight
75
+ !/images/meth/weight.gif!
76
+
77
+ * Missing genes are penalized using a penalty term
78
+ !/images/meth/penalty.gif! that will be used in the next formula
79
+
80
+ * The genes in the query list may be over-represented at the top of the
81
+ signature or at the bottom. We calculate a separate partial score for each
82
+ event, !/images/meth/PS_top.gif! and !/images/meth/PS_bottom.gif!, at each
83
+ position !/images/meth/i.gif!. !(large)/images/meth/PS_top_formula.gif! and
84
+ !(large)/images/meth/PS_bottom_formula.gif!
85
+
86
+ * The score assigned to the list (!/images/meth/S_up.gif! or
87
+ !/images/meth/S_down.gif!) is the maximum value in
88
+ !/images/meth/PS_top.gif! or !/images/meth/PS_bottom.gif!. If the value
89
+ comes from !/images/meth/PS_bottom.gif!, then the list score is made
90
+ negative
91
+
92
+ The previous process is used to generate !/images/meth/S_up.gif! and
93
+ !/images/meth/S_down.gif!, the scores for the up-regulated and
94
+ down-regulated gene lists. If one of the lists is empty its correspondent
95
+ score is 0. The final score for the query is 0 if both
96
+ !/images/meth/S_top.gif! and !/images/meth/S_bottom.gif! have the same sign
97
+ and are non-zero, or !/images/meth/S_diff.gif! if they have different
98
+ signs. Note that the sign of the final score indicates if the relationship
99
+ of the signature to the query is direct or inverse.
100
+
101
+ The significance of the score is established using a permutation test. The null
102
+ distribution is estimated by finding 1000 scores for random queries of the
103
+ same length as the original.
104
+
105
+ h3(#computations). Computational details
106
+
107
+ Each query in MARQ may be compared with two or three thousand different
108
+ signatures, which makes computation time an important issue. Each
109
+ comparison involves computing the score for the query genes and comparing
110
+ it to 1000 scores derived from selecting random sets of genes of the same
111
+ size to establish the score significance. In order to save computations,
112
+ the permutations scores are pooled for signatures of the same size. This is
113
+ possible thanks to the fact that the scores depend only on the positions of
114
+ the query genes, which are permuted, and the size of the signature, which
115
+ remains the same; since each dataset in each particular platform covers the
116
+ same probes, all their signatures derived from datasets of the same
117
+ platform have the same length. This enables us to compute the 1000
118
+ permutations scores once per platform, instead of once per signature, and
119
+ thus save plenty of time.
120
+
121
+
122
+ h3(#weight). Weight function
123
+
124
+ The vanilla version of the scoring function, as proposed in the
125
+ Connectivity Map, suffers from the problem that if query genes cluster
126
+ towards the center of the signature they receive a high score, which
127
+ is not commonly regarded as an interesting finding. The latest versions of
128
+ GSEA make use of the correlation with the phenotype to weight the
129
+ importance of genes, such that genes in the center of the signature will
130
+ not produce a high score since their weight will be small.
131
+
132
+ In MARQ, however, this alternative is unfeasible, since using the
133
+ correlation with the phenotype will no longer enable us to pool permutation
134
+ scores between signatures from the same platform. This happens because the
135
+ scores will now depend in values that are specific for each signature, as is
136
+ the case with the correlation with the phenotype, and the permutation scores
137
+ would follow different distributions and will cease to be exchangeable under
138
+ the null hypothesis, a requirement for permutation tests.
139
+
140
+ To avoid this problem, instead of the original correlation with the
141
+ phenotype, we define a weight function that serves a similar purpose,
142
+ weighting genes in the extremes more than genes towards the center, but
143
+ that would be the same for all signatures. In theory, any function that
144
+ achieves this goal could be appropriate, however, to remain faithful to the
145
+ original idea proposed in GSEA, we use a function that mimics the average
146
+ distribution of the log-ratios of the genes.
147
+
148
+ The following picture shows the values of the log-ratios for 50 signatures
149
+ selected at random. Genes are sorted by the log-ratios, the horizontal axis
150
+ shows the value of the distance !(large)/images/meth/d_noabs.gif! (in this
151
+ case we do not take the absolute value for illustration purposes) and the
152
+ vertical axis shows the absolute value of the log-ratio normalized to be in
153
+ the 0 to 1 range by dividing by the largest value (this normalization does
154
+ not affect the scores). Each black line represents one of the 50 signatures.
155
+ The red vertical lines show the places where the values change signs. The
156
+ blue line represents the average of the signature values at each point. As
157
+ we can see, the function is relatively symmetric and predictable, the sign
158
+ changes close to the center, and the shape is a slow increase in the middle
159
+ and a steep bump in the extremes
160
+
161
+ !(plot)/images/meth/Rplot.png!
162
+
163
+ The weight function we use is defined as
164
+ !(large)/images/meth/weight_function.gif!, in this case
165
+ !/images/meth/d.gif! is defined as "here":/help/methods#score, taken
166
+ the absolute value. The parameters for this function are fitted using
167
+ non-linear least squares. The results is the green line in the plot. The
168
+ values for the parameters are approximately !/images/meth/alpha.gif!
169
+ !/images/meth/beta_0.gif! !/images/meth/beta_1.gif!.
170
+
171
+ The data and R scripts to reproduce this analysis can be obtained
172
+ "here":/data/weights.tar.gz
173
+
174
+
175
+ h1(#translations). Translation system
176
+
177
+ Each organism has a file that specifies all the equivalences between gene
178
+ id formats. This file is built by merging information from the Entrez Gene
179
+ downloadable data files, data files available in organism specific
180
+ databases, such as SGD for yeast or MGI for mouse, and information
181
+ extracted from BioMart. In particular, all platform specific formats are
182
+ extracted from BioMart. Each organism has a configuration file specifying
183
+ all the data sources and how to process them, which is done automatically.
184
+ This information is updated periodically.
185
+
186
+ For each organism one of the id formats is selected as the native format.
187
+ This native format the target of all gene id translations, and glues all the
188
+ information regarding each gene in the system. The native format is selected
189
+ to have a wide coverage; it is usually the organism specific database id,
190
+ like SGD and MGI for yeast and mouse. For human the native format is Entrez
191
+ Gene.
192
+
193
+ The translation system takes each gene identifier and finds the
194
+ correspondent native format id. All the formats are sorted for relevance to
195
+ resolve matches; so if a gene identifier matches an _Entrez Gene Alias_ for
196
+ a particular gene, and a _Gene Symbol_ for another, the later is chosen,
197
+ since the _Entrez Gene Alias_ lists names not in favor anymore.
198
+
199
+ The translation system is used to translate probe ids and query genes for
200
+ cross platform queries. Each platform names its probes using a particular
201
+ id format, which may or may not be one of the formats included in our
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+ equivalence file. Fortunately, platforms usually include other information
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+ fields for the probes that list ids in other formats. It the primary probe
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+ id format is unknown, we search the other fields until we find one that we
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+ can translate. To determine if whether the primary format or any of the
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+ others are suitable for translation we perform the actual translation and
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+ count the number of different genes we translate to. We call the coverage
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+ of the translation to the number of target genes we reach. We use the
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+ coverage to select the field to use in the translation. Platforms with a
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+ coverage amounting to less than 10% of the original probe ids are
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+ considered not translatable by the system.
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+
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+ AILUN is also used for platform translations. The target format for AILUN
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+ is always Entrez Gene, which means that we need a second translation to our
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+ native format for all organisms except human, which already have Entrez as
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+ the native format. After this second translation we measure the coverage of
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+ both systems for that platform and select the best one.
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+
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+
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+ h1(#annotations). Signature Annotations
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+
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+ Each signature receives annotations of several types. Each annotation type
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+ defines a number of terms that are shared among different signatures. To
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+ determine if a term is significantly represented in the results signature
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+ list we use the same "score function":#score as with comparing signatures,
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+ in this case the signature list is like a signature itself and the
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+ individual signatures are like the genes.
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+
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+ Since some signatures may have their comparison levels swapped (see
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+ "comparisons":#comparisons) and end up in the wrong side of the list, we
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+ sort the signatures by the absolute score value, so all significant
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+ signatures end up at the top, regardless of the direction of the
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+ association with the query. This means, of course, that we only consider
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+ terms to be relevant if their appear in the top signatures, since the
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+ bottom signatures are actually at the middle of the table.
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+
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+ Also, some datasets with many factors and levels per factor may have a
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+ large number of signatures. Terms derived from the datasets description,
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+ for example, will be over-represented for that reason. Not only that, but
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+ often signatures from the same dataset tend to cluster together, which only
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+ aggravates the problem. To deal with this problem we consider differently
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+ terms derived from the datasets and thus common to all its signatures, and
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+ terms specific to each signature. Terms derived from the datasets are only
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+ considered for the best ranking signature.
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+
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+ This a brief description of the two types of annotations currently used
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+
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+ * Words: Each signature is annotated with the text from the datasets
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+ description and title, as well as the text from the levels been compared.
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+ As we discussed in a previous paragraph, the text from the levels is
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+ specific to the signature and always considered, while the text from the
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+ description and title of the dataset is only considered once. The text is
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+ parsed into words, the words are stemmed, and the resulting terms are used
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+ to annotate the signature. Terms that appear in more than 5% of the
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+ signatures are removed from the analysis, as they are to general to be
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+ interesting.
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+
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+
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+ *(#go_annotations) Gene Ontology: For each signature we extract the up and
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+ down regulated genes. For this we could make use of the t-values used to
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+ produce de signatures, but for simplicity's shake, we just take the 100
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+ first and the 100 bottom genes.
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+ This approach gave better results than using the t-values due to the fact
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+ that the t-values where missing on some signatures (due to lack of sample
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+ replicates) or their distribution varied so greatly that the sizes of the
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+ lists of significant genes where to diverse. Each signature is assigned a
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+ list of GO terms over-represented in the top genes and another list for the
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+ bottom genes, and similarly for GOSlim terms. We use the
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+ "GeneCodis":http://genecodis.dacya.ucm.es engine to find over-represented GO term
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+ for the category of _Biological Process_. For each query the 'directly
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+ related terms' are those that appear over-expressed in the top genes for
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+ signatures positively co-related to the query, and over-expressed in the
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+ bottom genes for signatures negatively co-related. Vice versa for the
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+ 'indirectly related terms'.
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+
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+
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+ h1. Rank Product Signature Comparisons
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+
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+ Two or more signatures can be compared using Rank Products. The Rank
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+ Product score is computed by multiplying the relative ranks of the gene in
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+ each of the signatures. The relative rank is the rank divided by the number
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+ of genes in the signature. Genes missing in any of the signatures are
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+ ignored.
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+
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+ The significance of a Rank Product score is established using a
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+ permutations test. We use a modification of the permutation test proposed
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+ in the standard Rank Product implementation: We sample the null
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+ distribution by drawing a random number from 0 to 1 representing the
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+ relative rank of a gene, one for each signature, and computing the score
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+ for those. We produce 5000 of this random scores. "Empirical
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+ tests":/data/RankProd.tar.gz show that these permutations follow the same
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+ distribution that scores drawn using the standard permutations used in the
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+ original implementation of Rank Product, and are more efficient. Note that
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+ this only works because our signatures are considered all to be from the
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+ same class. In the general two class case one still needs the complete
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+ permutation scheme.
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+
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+
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+
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+
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+