[BioC] Extracting genes associated to GO terms
paul [guest]
guest at bioconductor.org
Fri Oct 25 15:22:06 CEST 2013
I went through the following post https://stat.ethz.ch/pipermail/bioconductor/2013-July/054125.html. I have similar problems in extracting genes associated to GO terms but probesetsummary2 does not work as well.
This is what I did:
#### selected list of genes
structure(c("245062_at", "245107_at", "245137_at", "245178_at",
"245189_at", "245305_at", "245339_at", "245381_at", "245392_at",
"245411_at", "245412_at", "245414_at", "245504_at", "245505_at",
"245516_at", "245558_at", "245603_at", "245611_at", "245705_at",
"245749_at", "245758_at", "245863_s_at", "245877_at", "246002_at",
"246119_at", "246203_at", "246216_at", "246252_s_at", "246301_at",
"246312_at", "246338_s_at", "246448_at", "246499_at", "246535_at",
"246627_s_at", "246796_at", "246811_at", "246818_at", "246947_at",
"246984_at", "247033_at", "247132_at", "247134_at", "247210_at",
"247354_at", "247418_at", "247427_at", "247544_at", "247620_at",
"247637_at", "247797_at", "247950_at", "248040_at", "248071_at",
"248094_at", "248104_at", "248167_at", "248178_at", "248364_at",
"248424_at", "248428_at", "248462_at", "248472_at", "248604_at",
"248722_at", "248761_at", "248770_at", "248848_at", "249098_at",
"249102_at", "249104_at", "249199_at", "249359_at", "249601_at",
"249672_at", "249741_at", "249767_at", "249791_at", "249925_at",
"249995_at", "250046_at", "250094_at", "250107_at", "250182_at",
"250200_at", "250230_at", "250239_at", "250253_at", "250285_at",
"250330_at", "250363_at", "250380_at", "250395_at", "250458_s_at",
"250474_at", "250512_at", "250570_at", "250602_s_at", "250691_at",
"250697_at", "250717_at", "250770_at", "250781_at", "250828_at",
"250906_at", "250919_at", "250975_at", "251008_at", "251015_at",
"251042_at", "251259_at", "251301_at", "251328_at", "251479_at",
"251509_at", "251531_at", "251578_at", "251605_at", "251704_at",
"251824_at", "251862_at", "251866_at", "251918_at", "252209_at",
"252375_at", "252453_at", "252638_at", "252639_at", "252817_at",
"252950_at", "252983_at", "252984_at", "253040_at", "253075_at",
"253142_at", "253160_at", "253224_at", "253255_at", "253386_at",
"253401_at", "253468_at", "253494_at", "253572_at", "253589_at",
"253614_at", "253758_at", "253827_at", "253851_at", "253957_at",
"254015_at", "254048_at", "254121_at", "254155_at", "254197_at",
"254292_at", "254342_at", "254425_at", "254457_at", "254527_at",
"254536_at", "254556_at", "254560_at", "254667_at", "254693_at",
"254715_at", "254729_at", "254774_at", "254797_at", "254847_at",
"254867_at", "254914_at", "255053_at", "255120_x_at", "255297_x_at",
"255307_at", "255311_at", "255365_at", "255528_at", "255602_at",
"255625_at", "255649_at", "255684_at", "255723_at", "255739_at",
"255866_at", "255873_at", "255880_at", "255898_at", "255925_at",
"255994_at", "255995_at", "256119_at", "256217_at", "256326_at",
"256351_at", "256392_at", "256458_at", "256534_at", "256590_at",
"256724_at", "256746_at", "256823_at", "256906_at", "256919_at",
"256940_at", "256964_at", "256981_at", "256989_at", "257045_at",
"257088_at", "257171_at", "257205_at", "257268_at", "257335_at",
"257371_at", "257476_at", "257592_at", "257633_at", "257735_at",
"257738_at", "257765_at", "257772_at", "257858_at", "257972_at",
"258005_at", "258119_at", "258156_at", "258181_at", "258227_at",
"258269_at", "258289_at", "258557_at", "258565_at", "258574_at",
"258625_at", "258627_at", "258640_at", "258664_at", "258673_at",
"258743_s_at", "258793_at", "258794_at", "259036_at", "259182_at",
"259198_at", "259273_s_at", "259318_at", "259331_at", "259345_s_at",
"259359_at", "259379_at", "259390_at", "259409_at", "259414_at",
"259439_at", "259447_s_at", "259463_at", "259485_at", "259498_at",
"259500_at", "259518_at", "259574_at", "259668_at", "259682_at",
"259780_at", "259814_at", "259834_at", "259992_at", "260210_at",
"260328_at", "260334_at", "260335_at", "260347_at", "260393_at",
"260419_at", "260432_at", "260470_at", "260580_at", "260643_at",
"260903_at", "260936_at", "261107_at", "261110_at", "261127_at",
"261154_at", "261161_at", "261229_at", "261269_at", "261378_at",
"261426_at", "261481_at", "261498_at", "261577_at", "261640_at",
"261778_at", "261928_at", "261938_at", "261960_at", "261995_at",
"262130_at", "262202_at", "262220_at", "262225_at", "262250_at",
"262317_at", "262342_at", "262406_at", "262408_at", "262464_at",
"262522_at", "262643_at", "262708_at", "262770_at", "262788_at",
"262821_at", "262825_at", "262904_at", "263005_at", "263063_s_at",
"263075_at", "263096_at", "263127_at", "263212_at", "263225_at",
"263240_s_at", "263241_at", "263323_at", "263336_x_at", "263387_at",
"263570_at", "263586_at", "263593_at", "263805_at", "263946_at",
"263991_at", "264010_at", "264122_at", "264127_at", "264146_at",
"264200_at", "264202_at", "264266_at", "264524_at", "264560_at",
"264571_at", "264587_at", "264633_at", "264656_at", "264698_at",
"264794_at", "264832_at", "264852_at", "264937_at", "264979_s_at",
"265014_at", "265238_s_at", "265376_at", "265793_at", "266044_s_at",
"266048_at", "266065_at", "266126_at", "266207_at", "266268_at",
"266344_at", "266366_at", "266382_at", "266441_at", "266547_at",
"266597_at", "266607_at", "266651_at", "266694_at", "266776_at",
"266816_at", "266881_at", "266911_at", "266967_at", "267009_at",
"267010_at", "267136_at", "267330_at", "267375_at", "267457_at",
"267477_at", "267555_at", "267639_at", "AFFX-r2-At-Actin-M_s_at"
), .Names = c("245062_at", "245107_at", "245137_at", "245178_at",
"245189_at", "245305_at", "245339_at", "245381_at", "245392_at",
"245411_at", "245412_at", "245414_at", "245504_at", "245505_at",
"245516_at", "245558_at", "245603_at", "245611_at", "245705_at",
"245749_at", "245758_at", "245863_s_at", "245877_at", "246002_at",
"246119_at", "246203_at", "246216_at", "246252_s_at", "246301_at",
"246312_at", "246338_s_at", "246448_at", "246499_at", "246535_at",
"246627_s_at", "246796_at", "246811_at", "246818_at", "246947_at",
"246984_at", "247033_at", "247132_at", "247134_at", "247210_at",
"247354_at", "247418_at", "247427_at", "247544_at", "247620_at",
"247637_at", "247797_at", "247950_at", "248040_at", "248071_at",
"248094_at", "248104_at", "248167_at", "248178_at", "248364_at",
"248424_at", "248428_at", "248462_at", "248472_at", "248604_at",
"248722_at", "248761_at", "248770_at", "248848_at", "249098_at",
"249102_at", "249104_at", "249199_at", "249359_at", "249601_at",
"249672_at", "249741_at", "249767_at", "249791_at", "249925_at",
"249995_at", "250046_at", "250094_at", "250107_at", "250182_at",
"250200_at", "250230_at", "250239_at", "250253_at", "250285_at",
"250330_at", "250363_at", "250380_at", "250395_at", "250458_s_at",
"250474_at", "250512_at", "250570_at", "250602_s_at", "250691_at",
"250697_at", "250717_at", "250770_at", "250781_at", "250828_at",
"250906_at", "250919_at", "250975_at", "251008_at", "251015_at",
"251042_at", "251259_at", "251301_at", "251328_at", "251479_at",
"251509_at", "251531_at", "251578_at", "251605_at", "251704_at",
"251824_at", "251862_at", "251866_at", "251918_at", "252209_at",
"252375_at", "252453_at", "252638_at", "252639_at", "252817_at",
"252950_at", "252983_at", "252984_at", "253040_at", "253075_at",
"253142_at", "253160_at", "253224_at", "253255_at", "253386_at",
"253401_at", "253468_at", "253494_at", "253572_at", "253589_at",
"253614_at", "253758_at", "253827_at", "253851_at", "253957_at",
"254015_at", "254048_at", "254121_at", "254155_at", "254197_at",
"254292_at", "254342_at", "254425_at", "254457_at", "254527_at",
"254536_at", "254556_at", "254560_at", "254667_at", "254693_at",
"254715_at", "254729_at", "254774_at", "254797_at", "254847_at",
"254867_at", "254914_at", "255053_at", "255120_x_at", "255297_x_at",
"255307_at", "255311_at", "255365_at", "255528_at", "255602_at",
"255625_at", "255649_at", "255684_at", "255723_at", "255739_at",
"255866_at", "255873_at", "255880_at", "255898_at", "255925_at",
"255994_at", "255995_at", "256119_at", "256217_at", "256326_at",
"256351_at", "256392_at", "256458_at", "256534_at", "256590_at",
"256724_at", "256746_at", "256823_at", "256906_at", "256919_at",
"256940_at", "256964_at", "256981_at", "256989_at", "257045_at",
"257088_at", "257171_at", "257205_at", "257268_at", "257335_at",
"257371_at", "257476_at", "257592_at", "257633_at", "257735_at",
"257738_at", "257765_at", "257772_at", "257858_at", "257972_at",
"258005_at", "258119_at", "258156_at", "258181_at", "258227_at",
"258269_at", "258289_at", "258557_at", "258565_at", "258574_at",
"258625_at", "258627_at", "258640_at", "258664_at", "258673_at",
"258743_s_at", "258793_at", "258794_at", "259036_at", "259182_at",
"259198_at", "259273_s_at", "259318_at", "259331_at", "259345_s_at",
"259359_at", "259379_at", "259390_at", "259409_at", "259414_at",
"259439_at", "259447_s_at", "259463_at", "259485_at", "259498_at",
"259500_at", "259518_at", "259574_at", "259668_at", "259682_at",
"259780_at", "259814_at", "259834_at", "259992_at", "260210_at",
"260328_at", "260334_at", "260335_at", "260347_at", "260393_at",
"260419_at", "260432_at", "260470_at", "260580_at", "260643_at",
"260903_at", "260936_at", "261107_at", "261110_at", "261127_at",
"261154_at", "261161_at", "261229_at", "261269_at", "261378_at",
"261426_at", "261481_at", "261498_at", "261577_at", "261640_at",
"261778_at", "261928_at", "261938_at", "261960_at", "261995_at",
"262130_at", "262202_at", "262220_at", "262225_at", "262250_at",
"262317_at", "262342_at", "262406_at", "262408_at", "262464_at",
"262522_at", "262643_at", "262708_at", "262770_at", "262788_at",
"262821_at", "262825_at", "262904_at", "263005_at", "263063_s_at",
"263075_at", "263096_at", "263127_at", "263212_at", "263225_at",
"263240_s_at", "263241_at", "263323_at", "263336_x_at", "263387_at",
"263570_at", "263586_at", "263593_at", "263805_at", "263946_at",
"263991_at", "264010_at", "264122_at", "264127_at", "264146_at",
"264200_at", "264202_at", "264266_at", "264524_at", "264560_at",
"264571_at", "264587_at", "264633_at", "264656_at", "264698_at",
"264794_at", "264832_at", "264852_at", "264937_at", "264979_s_at",
"265014_at", "265238_s_at", "265376_at", "265793_at", "266044_s_at",
"266048_at", "266065_at", "266126_at", "266207_at", "266268_at",
"266344_at", "266366_at", "266382_at", "266441_at", "266547_at",
"266597_at", "266607_at", "266651_at", "266694_at", "266776_at",
"266816_at", "266881_at", "266911_at", "266967_at", "267009_at",
"267010_at", "267136_at", "267330_at", "267375_at", "267457_at",
"267477_at", "267555_at", "267639_at", "AFFX-r2-At-Actin-M_s_at"
))
#### Universe is the entire set of genes from the ATH1 chip (22810 genes)
pos8<-unlist(mget(new,ath1121501ACCNUM,ifnotfound=NA))
poss8 <- new("GOHyperGParams", geneIds = pos8, universeGeneIds =locus, annotation="ath1121501",
ontology = "BP", pvalueCutoff = 0.05, conditional = FALSE, testDirection = "over")
posss8 <- hyperGTest(poss8)
htmlReport(posss8, file = "pos8.html")
When I run this and do probeSetSummary2(posss8)
I get the warning message:
Warning message:
The vector of geneIds used to create the GOHyperGParamsobject was not a named vector.
If you want to know theprobesets that contributed to this result either usea named vector for geneIds, or pass a vector of probeset IDs via sigProbesets.
And the result has GO terms which were not present in the HTML table.
-- output of sessionInfo():
R version 3.0.1 (2013-05-16)
Platform: x86_64-redhat-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8
[4] LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=C LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] parallel stats graphics grDevices utils datasets methods base
other attached packages:
[1] ath1121501.db_2.9.0 org.At.tair.db_2.9.0 GO.db_2.9.0 GOstats_2.26.0
[5] RSQLite_0.11.4 DBI_0.2-5 graph_1.38.3 Category_2.26.0
[9] AnnotationDbi_1.22.6 Biobase_2.20.1 BiocGenerics_0.6.0
loaded via a namespace (and not attached):
[1] annotate_1.38.0 AnnotationForge_1.2.2 genefilter_1.42.0 GSEABase_1.22.0
[5] IRanges_1.18.4 RBGL_1.36.2 splines_3.0.1 stats4_3.0.1
[9] survival_2.37-4 tools_3.0.1 XML_3.98-1.1 xtable_1.7-1
--
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