# HG changeset patch # User lecorguille # Date 1438695967 14400 # Node ID e646ad125f2d6bb79b6b8e036cde09dbebf9d00a # Parent 8dd2a438bfba792eb71d7115a4246f45ecd9aa21 Add test diff -r 8dd2a438bfba -r e646ad125f2d abims_anova.xml --- a/abims_anova.xml Tue Jun 30 06:02:46 2015 -0400 +++ b/abims_anova.xml Tue Aug 04 09:46:07 2015 -0400 @@ -1,14 +1,17 @@ - - - - Rscript - batch - + N-way anova. With ou Without interactions + + + Rscript + + + + + - abims_anova.r file "$input" sampleinfo "$sampleinfo" mode "$mode" +abims_anova.r file "$input" sampleinfo "$sampleinfo" mode "$mode" condition "c('$condition_1' #for $i, $s in enumerate( $conditions ) ,'${s.condition}' @@ -21,58 +24,72 @@ - - Mode - - - - - - - - + + Mode + + + + + + + + - - - - PValue adjusted method - - - - - - - - - + + + + PValue adjusted method + + + + + + + + + - Selection method - - - + Selection method + + + - Separator of columns - - - - + Separator of columns + + + + - - + + - - - - + + + + + + + + + + + + + + + + + + @@ -117,23 +134,23 @@ ***.anova_pvalue.tabular** - | A tabular file which represents for each metabolite (row), the value of the intensity in each sample (column) + two columns (aovPValue and aovAdjPValue). + | A tabular file which represents for each metabolite (row), the value of the intensity in each sample (column) + two columns (aovPValue and aovAdjPValue). ***.anova_filtered.tabular** - | The tabular file xset.anova_pvalue.tabular containing only the metabolites that have been filtered by aovAdjPValue. - - + | The tabular file xset.anova_pvalue.tabular containing only the metabolites that have been filtered by aovAdjPValue. + + ------ .. class:: infomark The outputs ***.anova_filtered.tabular** or ***.anova_pvalue.tabular** are tabular files. You can continue your analysis using it in the following tools: - | PCA - | Hierarchical Clustering + | PCA + | Hierarchical Clustering - - + + --------------------------------------------------- --------------- @@ -145,7 +162,7 @@ ----------- **>A part of an example of Data Matrix file input** - + +--------+------------------+----------------+ | Name | Bur-eH_FSP_12 | Bur-eH_FSP_24 | @@ -156,8 +173,8 @@ +--------+------------------+----------------+ **>A part of an example of Sample Metadata file input** - - + + +---------------------------+------------+------------+------------+ | Sample name | class | time | batch | +===========================+============+============+============+ @@ -173,13 +190,13 @@ Parameters ---------- - | Mode -> **row** - | column name of condition -> **class** - | Separator of columns: -> **tabulation** - | Decimal separator -> **.** - | PValue adjusted method -> **BH** - | Threshold -> **0.001** - + | Mode -> **row** + | column name of condition -> **class** + | Separator of columns: -> **tabulation** + | Decimal separator -> **.** + | PValue adjusted method -> **BH** + | Threshold -> **0.001** + Output files @@ -194,6 +211,11 @@ .. image:: anova_filtered.png + + + Ronald A. Fisher in the 1930s + + diff -r 8dd2a438bfba -r e646ad125f2d static/images/anova_workflow.png Binary file static/images/anova_workflow.png has changed diff -r 8dd2a438bfba -r e646ad125f2d static/images/hclust.png Binary file static/images/hclust.png has changed diff -r 8dd2a438bfba -r e646ad125f2d static/images/pca_abims_Rplots.png Binary file static/images/pca_abims_Rplots.png has changed diff -r 8dd2a438bfba -r e646ad125f2d static/images/pca_abims_Rplots1.png Binary file static/images/pca_abims_Rplots1.png has changed diff -r 8dd2a438bfba -r e646ad125f2d static/images/pca_abims_eigenvalue.png Binary file static/images/pca_abims_eigenvalue.png has changed diff -r 8dd2a438bfba -r e646ad125f2d static/images/pca_abims_percentage_of_variance.png Binary file static/images/pca_abims_percentage_of_variance.png has changed diff -r 8dd2a438bfba -r e646ad125f2d test-data/dataMatrix.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/dataMatrix.tsv Tue Aug 04 09:46:07 2015 -0400 @@ -0,0 +1,16 @@ +dataMatrix HU_017 HU_028 HU_034 HU_051 HU_060 HU_078 HU_091 HU_093 HU_099 HU_110 HU_130 HU_134 HU_138 HU_149 HU_152 HU_175 HU_178 HU_185 HU_204 HU_208 +HMDB03193 76043 412165 44943 27242 436566 173175 242549 57066 559869 3732 339188 471368 262271 127285 451270 212500 79673 NA 891129 43907 +HMDB01101 30689 6877586 52217 3158 10789748 229568 4763576 3878773 976436 831937 608298 1605075 72021 442510 1107705 1464339 31250 2724553 72900 32742 +HMDB10348 47259 544877 60885 34582 529874 168264 176500 76457 610110 16262 279156 524468 451573 591487 433529 161069 214392 13781 1580343 39315 +HMDB59717 357351 1030464 301983 67604 306862 1028110 1530493 270027 1378535 289677 808334 1132813 871209 895435 715190 1563158 784738 146195 994336 239030 +HMDB00822 483755 579287 1132413 157113 1577570 1469735 1085454 477909 814755 245417 610681 763706 2406336 827531 992508 569605 355321 150259 1334200 271010 +HMDB13189 2644620 727587 1661412 619181 136278 2755434 593863 837865 3526136 2003278 1608814 3446611 1941527 113937 3132404 2893445 2092753 1034666 1517319 841661 +HMDB00299 250551 1046138 456162 159386 1013302 808657 614370 250403 768004 242085 504108 1014041 1362408 1057660 1110050 566050 411886 142233 1992420 284775 +HMDB00191 560002 771533 575790 392284 888498 785428 645785 591569 960658 910201 639437 1092885 1409045 2292023 1246459 1945577 710519 773384 1061418 622898 +HMDB00518 34236 58249 85944 NA 342102 129886 175800 13154 230242 NA 440223 315368 10657 419508 48673 28361 514579 23108 867108 73831 +HMDB00715 1252089 2547452 905408 371059 4983588 5140022 2658555 814523 2558923 859466 4184204 3865723 3236644 2615560 3820724 3577833 2295288 625924 7517724 1341900 +HMDB01032 2569205 26023086 1604999 430453 8103558 26222916 257139 675754 59906109 263055 31151730 18648127 14989438 1554658 20249262 5588731 871010 15920 9120781 44276 +HMDB00208 747080 13420742 595872 1172376 7172632 3143654 4059767 1433702 5593888 5402629 2477288 3346077 4230072 7621236 8960828 10335722 7037373 1574738 3359238 2540044 +HMDB04824 374028 1144386 539206 178517 1046190 959381 605191 310260 1253319 477259 477995 825691 1157093 1089284 1411802 1020206 782673 346761 1824553 387811 +HMDB00512 53304 319783 280560 85009 1333877 556003 590779 209285 342532 198512 569970 525240 246282 1140422 542345 1171008 827723 222953 438839 85554 +HMDB00251 368600 616555 94936 622468 180988 293988 352855 767894 268331 167246 310918 1248919 577184 10985 335711 403815 80614 63393 454489 616061 diff -r 8dd2a438bfba -r e646ad125f2d test-data/dataMatrix.tsv_anova_filtered.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/dataMatrix.tsv_anova_filtered.tabular Tue Aug 04 09:46:07 2015 -0400 @@ -0,0 +1,3 @@ + HU_017 HU_028 HU_034 HU_051 HU_060 HU_078 HU_091 HU_093 HU_099 HU_110 HU_130 HU_134 HU_138 HU_149 HU_152 HU_175 HU_178 HU_185 HU_204 HU_208 +HMDB00208 747080 13420742 595872 1172376 7172632 3143654 4059767 1433702 5593888 5402629 2477288 3346077 4230072 7621236 8960828 10335722 7037373 1574738 3359238 2540044 +HMDB00512 53304 319783 280560 85009 1333877 556003 590779 209285 342532 198512 569970 525240 246282 1140422 542345 1171008 827723 222953 438839 85554 diff -r 8dd2a438bfba -r e646ad125f2d test-data/dataMatrix.tsv_anova_pvalue.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/dataMatrix.tsv_anova_pvalue.tabular Tue Aug 04 09:46:07 2015 -0400 @@ -0,0 +1,16 @@ + HU_017 HU_028 HU_034 HU_051 HU_060 HU_078 HU_091 HU_093 HU_099 HU_110 HU_130 HU_134 HU_138 HU_149 HU_152 HU_175 HU_178 HU_185 HU_204 HU_208 pvalueadjusted.BH.age pvalueadjusted.BH.gender +HMDB03193 76043 412165 44943 27242 436566 173175 242549 57066 559869 3732 339188 471368 262271 127285 451270 212500 79673 NA 891129 43907 0.740856975457218 0.740856975457218 +HMDB01101 30689 6877586 52217 3158 10789748 229568 4763576 3878773 976436 831937 608298 1605075 72021 442510 1107705 1464339 31250 2724553 72900 32742 0.347623051099051 0.234554902330543 +HMDB10348 47259 544877 60885 34582 529874 168264 176500 76457 610110 16262 279156 524468 451573 591487 433529 161069 214392 13781 1580343 39315 0.720303175717481 0.720303175717481 +HMDB59717 357351 1030464 301983 67604 306862 1028110 1530493 270027 1378535 289677 808334 1132813 871209 895435 715190 1563158 784738 146195 994336 239030 0.252979062487671 0.517822514350462 +HMDB00822 483755 579287 1132413 157113 1577570 1469735 1085454 477909 814755 245417 610681 763706 2406336 827531 992508 569605 355321 150259 1334200 271010 0.808532959173048 0.808532959173048 +HMDB13189 2644620 727587 1661412 619181 136278 2755434 593863 837865 3526136 2003278 1608814 3446611 1941527 113937 3132404 2893445 2092753 1034666 1517319 841661 0.329174238111018 0.329174238111018 +HMDB00299 250551 1046138 456162 159386 1013302 808657 614370 250403 768004 242085 504108 1014041 1362408 1057660 1110050 566050 411886 142233 1992420 284775 0.995859884733937 0.995859884733937 +HMDB00191 560002 771533 575790 392284 888498 785428 645785 591569 960658 910201 639437 1092885 1409045 2292023 1246459 1945577 710519 773384 1061418 622898 0.15341384456659 0.15341384456659 +HMDB00518 34236 58249 85944 NA 342102 129886 175800 13154 230242 NA 440223 315368 10657 419508 48673 28361 514579 23108 867108 73831 0.439012867631325 0.596200901535843 +HMDB00715 1252089 2547452 905408 371059 4983588 5140022 2658555 814523 2558923 859466 4184204 3865723 3236644 2615560 3820724 3577833 2295288 625924 7517724 1341900 0.814406453193777 0.814406453193777 +HMDB01032 2569205 26023086 1604999 430453 8103558 26222916 257139 675754 59906109 263055 31151730 18648127 14989438 1554658 20249262 5588731 871010 15920 9120781 44276 0.288354536353544 0.288354536353544 +HMDB00208 747080 13420742 595872 1172376 7172632 3143654 4059767 1433702 5593888 5402629 2477288 3346077 4230072 7621236 8960828 10335722 7037373 1574738 3359238 2540044 0.659785284053633 0.00376251274734483 +HMDB04824 374028 1144386 539206 178517 1046190 959381 605191 310260 1253319 477259 477995 825691 1157093 1089284 1411802 1020206 782673 346761 1824553 387811 0.646714644805001 0.646714644805001 +HMDB00512 53304 319783 280560 85009 1333877 556003 590779 209285 342532 198512 569970 525240 246282 1140422 542345 1171008 827723 222953 438839 85554 0.13976111393526 0.0491480895853803 +HMDB00251 368600 616555 94936 622468 180988 293988 352855 767894 268331 167246 310918 1248919 577184 10985 335711 403815 80614 63393 454489 616061 0.565910223149305 0.565910223149305 diff -r 8dd2a438bfba -r e646ad125f2d test-data/sampleMetadata.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sampleMetadata.tsv Tue Aug 04 09:46:07 2015 -0400 @@ -0,0 +1,21 @@ +sampleMetadata injectionOrder mode age bmi gender +HU_017 2 pos 40-50 23.03 M +HU_028 7 pos 40-50 23.92 F +HU_034 9 pos 50-60 23.37 M +HU_051 20 pos 20-30 23.23 F +HU_060 24 pos 50-60 28.72 F +HU_078 34 pos 40-50 25.18 M +HU_091 42 pos 60-70 26.12 M +HU_093 43 pos 50-60 21.71 M +HU_099 46 pos 20-30 21.3 M +HU_110 53 pos 50-60 20.9 F +HU_130 63 pos 30-40 26.06 M +HU_134 67 pos 40-50 22.89 M +HU_138 68 pos 40-50 21.88 M +HU_149 72 pos 30-40 19.49 F +HU_152 75 pos 20-30 17.58 F +HU_175 87 pos 30-40 21.26 F +HU_178 88 pos 60-70 32.87 F +HU_185 95 pos 40-50 21.09 F +HU_204 104 pos 30-40 29.06 M +HU_208 106 pos 20-30 18.61 F