[BioC] Error in extracting genes from Goterms using GOStats package

Sandy [guest] guest at bioconductor.org
Sun Jul 28 14:55:23 CEST 2013


I used the GOStats package on the following data:

locus<-c("261166_s_at", "263208_at", "263204_at", "263203_at", 
+          "263206_at", "260998_at", "264320_at", "264165_at", "264162_at", 
+          "263786_at", "262347_at", "261407_at", "263869_at", "260562_at", 
+          "260801_at", "258988_at", "258983_at", "262407_at", "260315_at", 
+          "259125_at", "261371_at", "261418_at", "255821_at", "255784_at", 
+          "255498_at", "259191_at", "259137_at", "262360_at", "262071_at", 
+          "255684_at", "261511_at", "263729_at", "264413_s_at", "264381_at", 
+          "264532_at", "260860_at", "263233_at", "263959_at", "255868_at", 
+          "262780_at", "246214_at", "260782_at", "260756_at", "260875_at", 
+          "259247_at", "263943_at", "260112_at", "262010_at", "255851_at", 
+          "246557_at", "261444_at", "264562_at", "264556_at", "259257_at", 
+          "261731_s_at", "260217_at", "260192_at", "255861_at", "264582_at", 
+          "261639_at", "261669_at", "255928_at", "255920_at", "259250_at", 
+          "255734_at", "263950_at", "264625_at", "264623_at", "259935_at", 
+          "261892_at", "261498_at", "256086_at", "263993_at", "261859_at", 
+          "260033_at", "259999_at", "261309_at", "259375_at", "260374_at", 
+          "260346_at", "262693_at", "263827_at", "262453_at", "262505_at", 
+          "265220_at", "265221_s_at", "265338_at", "266167_at", "263030_at", 
+          "262897_at", "265511_at", "265956_at", "263146_at", "264850_at", 
+          "264107_s_at", "264838_at", "266163_at", "264787_at", "264758_at", 
+          "263552_x_at", "263550_at", "263284_at", "263304_at", "263093_at", 
+          "263412_at", "262978_at", "266292_at", "265783_at", "265723_at", 
+          "265674_at", "263599_at", "265761_at", "266744_at", "266900_at", 
+          "266596_at", "266594_at", "262806_at", "265159_at", "267027_at", 
+          "245166_at", "245162_at", "245167_s_at", "266885_at", "266472_at", 
+          "266456_at", "266101_at", "262838_at", "263458_at", "263461_at", 
+          "264711_at", "263376_at", "265575_at", "265881_at", "266431_at", 
+          "260101_at", "267060_at", "267064_at", "265913_at", "260151_at", 
+          "260159_at", "266377_at", "245173_at", "258895_at", "258586_s_at", 
+          "258491_at", "258120_at", "258123_at", "258253_at", "258446_at", 
+          "267084_at", "267075_at", "258223_at", "267076_at", "267077_at", 
+          "267083_at", "258723_at", "258722_at", "258739_s_at", "258528_at", 
+          "258481_at", "258190_at", "258873_at", "258312_at", "258634_at", 
+          "258637_at", "258607_at", "258346_at", "258291_at", "258283_at", 
+          "258565_at", "258773_at", "255957_at", "258407_at", "255949_at", 
+          "257351_at", "257262_at", "257260_at", "257855_at", "257853_at", 
+          "256885_at", "256887_at", "256882_at", "257871_at", "257449_at", 
+          "258949_at", "258948_at", "258079_at", "258056_at", "257808_at", 
+          "257801_at", "257798_at", "257400_s_at", "257585_at", "256321_at", 
+          "256796_at", "257325_at", "256451_s_at", "257983_at", "256518_at", 
+          "256582_at", "257732_at", "256819_at", "252668_at", "252500_at", 
+          "252510_at", "252398_at", "252357_at", "252241_at", "252208_at", 
+          "252135_at", "252132_at", "252070_at", "252074_at", "246254_at", 
+          "256372_at", "256369_at", "251900_at", "251858_at", "251867_at", 
+          "251839_at", "251784_at", "251692_s_at", "251686_at", "251642_at", 
+          "251633_at", "251647_at", "251583_at", "251516_s_at", "251449_at", 
+          "251387_at", "251251_at", "251197_at", "251178_at", "251125_at", 
+          "255402_at", "255357_at", "255298_at", "255280_at", "255203_at", 
+          "255186_at", "254997_s_at", "254827_at", "254844_at", "254718_at", 
+          "254663_at", "254606_at", "254588_at", "254449_at", "245350_at", 
+          "245309_at", "245264_at", "245285_s_at", "245386_at", "245287_at", 
+          "245293_at", "254465_at", "254228_at", "254012_at", "254002_at", 
+          "253953_at", "253935_at", "253922_at", "253868_at", "253693_at", 
+          "253660_at", "253503_at", "253482_at", "253498_at", "253407_at", 
+          "253326_at", "253291_at", "253242_at", "253121_at", "253087_at", 
+          "253045_at", "253062_at", "253035_at", "252990_at", "252978_at", 
+          "252833_at", "252818_at", "252793_at", "252707_at", "252655_at", 
+          "252648_at", "250853_s_at", "250854_at", "250832_at", "250791_at", 
+          "250689_at", "250530_at", "250445_at", "245996_at", "250399_at", 
+          "250367_s_at", "267074_s_at", "267073_at", "267080_at", "267072_at", 
+          "250323_at", "267082_at", "267081_at", "250305_at", "250250_at", 
+          "250242_at", "250199_at", "250182_at", "250101_at", "250103_at", 
+          "250110_at", "250121_at", "250077_at", "250074_at", "250012_x_at", 
+          "246485_at", "250028_at", "246450_at", "246477_at", "246442_at", 
+          "249994_at", "249925_at", "245912_at", "245902_at", "246031_at", 
+          "246029_at", "245965_at", "246140_at", "246136_at", "249786_at", 
+          "249701_at", "249688_at", "249689_at", "246843_at", "246746_at", 
+          "246775_at", "246751_at", "246661_at", "246656_at", "246547_at", 
+          "249583_at", "249550_at", "249503_at", "249393_at", "249394_at", 
+          "249349_at", "249346_at", "249225_at", "249155_at", "249118_at", 
+          "249068_at", "249062_at", "249073_at", "248960_at", "248936_at", 
+          "248712_at", "248609_at", "248618_at", "248573_at", "248501_at", 
+          "248372_at", "248262_at", "248192_at", "248187_at", "248171_at", 
+          "248122_at", "247954_at", "247571_at", "247520_at", "247407_at", 
+          "247378_at", "247349_at", "247297_at", "247246_at", "247215_at", 
+          "247128_at", "247098_at", "246994_at", "246976_s_at", "246978_at", 
+          "246925_at", "244943_at", "244925_at"))

seltn<- seltpn<-c("263208_at", "263204_at", "260998_at", "264320_at", "264165_at", 
+                             "264162_at", "263786_at", "261407_at", "263869_at", "260801_at", 
+                              "258988_at", "258983_at", "262407_at", "259125_at", "261371_at", 
+                              "261418_at", "255821_at", "259191_at", "259137_at", "262360_at", 
+                              "262071_at", "255684_at", "261511_at", "264413_s_at", "264381_at", 
+                              "260860_at", "263233_at", "263959_at", "246214_at", "260782_at", 
+                              "259247_at", "262010_at", "246557_at", "261444_at", "264562_at", 
+                              "259257_at", "261731_s_at", "255861_at", "255928_at", "259250_at", 
+                              "255734_at", "264625_at", "264623_at", "261892_at", "261498_at", 
+                              "259999_at", "261309_at", "259375_at", "260346_at", "263827_at", 
+                              "265220_at", "265221_s_at", "265338_at", "266167_at", "263030_at", 
+                              "262897_at", "265511_at", "263146_at", "264850_at", "264107_s_at") 

seltpbn <- new("GOHyperGParams", geneIds = seltxxn, universeGeneIds =locus, annotation="ath1121501", 
                ontology = "BP", pvalueCutoff = 0.05, conditional = FALSE, testDirection = "over")
hgOver<- hyperGTest(seltpbn)

When I use ne to GO BP  test for over-representation 
677 GO BP ids tested (30 have p < 0.05)
Selected gene set size: 46 
    Gene universe size: 315 
    Annotation package: ath1121501 

But when I would like to extract the genes associated with a particular GO term, I get the following error:


Error in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function ‘cols’ for signature ‘"function"’

I do not understand where am going wrong. I just need to extract those genes that are associated with the GO Term from hgOver. I tried using 

geneIdsByCategory(hgOver, 'GO id') but this does not give me the list of genes from the selected list ( seltn) but instead that of the universe that are associated with the term

 -- output of sessionInfo(): 

R version 3.0.1 (2013-05-16)
Platform: x86_64-redhat-linux-gnu (64-bit)

 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8    LC_PAPER=C                 LC_NAME=C                 

attached base packages:
[1] grid      parallel  stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] gplots_2.11.3        MASS_7.3-27          KernSmooth_2.23-10   caTools_1.14         gdata_2.13.2        
 [6] gtools_3.0.0         plotrix_3.5          GO.db_2.9.0          ath1121501.db_2.9.0  org.At.tair.db_2.9.0
[11] GOstats_2.26.0       RSQLite_0.11.4       DBI_0.2-5            graph_1.38.3         Category_2.26.0     
[16] AnnotationDbi_1.22.1 affy_1.38.1          Biobase_2.20.0       BiocGenerics_0.6.0  

loaded via a namespace (and not attached):
 [1] affyio_1.28.0         annotate_1.38.0       AnnotationForge_1.2.2 BiocInstaller_1.10.3  bitops_1.0-5         
 [6] genefilter_1.42.0     GSEABase_1.22.0       IRanges_1.18.0        preprocessCore_1.22.0 RBGL_1.36.2          
[11] splines_3.0.1         stats4_3.0.1          survival_2.37-4       tools_3.0.1           XML_3.98-1.1         
[16] xtable_1.7-1          zlibbioc_1.6.0       

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