[BioC] Problem with invalid GO term in HyperGResult object - NOT solved

Jenny Drnevich drnevich at uiuc.edu
Fri Sep 14 18:38:09 CEST 2007


Hi Seth,

I had a problem earlier with an invalid GO term that was throwing up 
an error. You advised to update all my packages, which I thought 
solved the problem. However, the problem reappeared later when I 
reran my script, and I've figured out the difference is what other 
packages I have loaded. I have a complete R session below, where I 
first only load GOstats, then call hyperGTest on a GOHyperGParams 
object, which tests 1139 GO BP ids, and 44 have p < 0.001. Next I 
load affycoretools, then call hyperGTest on the exact same object, 
which now tests 1146 GO BP ids, and 46 have p < 0.001. Loading 
affycoretools in turn loads package GO, which then masks many 
functions from package GO.db - maybe this is where the problem 
is?  I'm fine because I can get the problematic GO term to disappear, 
but it seems like the discordance between the packages is a bug.

Thanks,
Jenny


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 > setwd("C:/statistics/anshuman")
 > load("anshuman2.RData")
 > library(GOstats)
Loading required package: graph
Loading required package: GO.db
Loading required package: AnnotationDbi
Loading required package: Biobase
Loading required package: tools

Welcome to Bioconductor

   Vignettes contain introductory material. To view, type
   'openVignette()'. To cite Bioconductor, see
   'citation("Biobase")' and for packages 'citation(pkgname)'.

Loading required package: DBI
Loading required package: RSQLite
Loading required package: annotate
Loading required package: RBGL
Loading required package: Category
Loading required package: genefilter
Loading required package: survival
Loading required package: splines
 > library(ath1121501)

Attaching package: 'ath1121501'


         The following object(s) are masked _by_ .GlobalEnv :

          ath1121501ENTREZID


 > SVC.up.BP.results.cond <- hyperGTest(SVC.up.BP.cond)
 > SVC.up.BP.results.cond
Gene to GO BP Conditional test for over-representation
1139 GO BP ids tested (44 have p < 0.001)
Selected gene set size: 1603
     Gene universe size: 12763
     Annotation package: ath1121501
 > sessionInfo()
R version 2.6.0 Under development (unstable) (2007-08-28 r42679)
i386-pc-mingw32

locale:
LC_COLLATE=English_United States.1252;LC_CTYPE=English_United 
States.1252;LC_MONETARY=English_United 
States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252

attached base packages:
[1] splines   tools     stats     graphics  grDevices utils     datasets
[8] methods   base

other attached packages:
  [1] ath1121501_1.17.0    GOstats_2.3.16       Category_2.3.36
  [4] genefilter_1.15.11   survival_2.32        RBGL_1.13.6
  [7] annotate_1.15.7      GO.db_1.17.1         AnnotationDbi_0.1.14
[10] RSQLite_0.6-2        DBI_0.2-3            Biobase_1.15.33
[13] graph_1.15.16

loaded via a namespace (and not attached):
[1] cluster_1.11.7     simpleaffy_2.13.01

 > library(affycoretools)
Loading required package: affy
Loading required package: affyio
Loading required package: preprocessCore
Loading required package: limma
Loading required package: biomaRt
Loading required package: XML

Attaching package: 'XML'


         The following object(s) are masked from package:graph :

          addNode

Loading required package: RCurl

Attaching package: 'biomaRt'


         The following object(s) are masked from package:annotate :

          getGO

Loading required package: gcrma
Loading required package: matchprobes
Loading required package: xtable
Loading required package: annaffy
Loading required package: GO

Attaching package: 'GO'


         The following object(s) are masked from package:GO.db :

          GOBPANCESTOR,
          GOBPCHILDREN,
          GOBPOFFSPRING,
          GOBPPARENTS,
          GOCCANCESTOR,
          GOCCCHILDREN,
          GOCCOFFSPRING,
          GOCCPARENTS,
          GOMAPCOUNTS,
          GOMFANCESTOR,
          GOMFCHILDREN,
          GOMFOFFSPRING,
          GOMFPARENTS,
          GOOBSOLETE,
          GOSYNONYM,
          GOTERM

Loading required package: KEGG
 > SVC.up.BP.results.cond <- hyperGTest(SVC.up.BP.cond)
 > SVC.up.BP.results.cond
Gene to GO BP Conditional test for over-representation
1146 GO BP ids tested (46 have p < 0.001)
Selected gene set size: 1603
     Gene universe size: 12766
     Annotation package: ath1121501
 > sessionInfo()
R version 2.6.0 Under development (unstable) (2007-08-28 r42679)
i386-pc-mingw32

locale:
LC_COLLATE=English_United States.1252;LC_CTYPE=English_United 
States.1252;LC_MONETARY=English_United 
States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252

attached base packages:
[1] splines   tools     stats     graphics  grDevices utils     datasets
[8] methods   base

other attached packages:
  [1] affycoretools_1.9.4    annaffy_1.9.4          KEGG_1.17.0
  [4] GO_1.17.0              xtable_1.5-1           gcrma_2.9.1
  [7] matchprobes_1.9.10     biomaRt_1.11.9         RCurl_0.8-1
[10] XML_1.9-0              limma_2.11.12          affy_1.15.8
[13] preprocessCore_0.99.13 affyio_1.5.10          ath1121501_1.17.0
[16] GOstats_2.3.16         Category_2.3.36        genefilter_1.15.11
[19] survival_2.32          RBGL_1.13.6            annotate_1.15.7
[22] GO.db_1.17.1           AnnotationDbi_0.1.14   RSQLite_0.6-2
[25] DBI_0.2-3              Biobase_1.15.33        graph_1.15.16

loaded via a namespace (and not attached):
[1] cluster_1.11.7     simpleaffy_2.13.01
 >


At 01:41 PM 9/11/2007, Jenny Drnevich wrote:
>Hi Seth,
>
>Once again, updating packages solved the problem!  They must have
>been VERY recent updates - I only installed R-devel last week! I
>guess that's the nature of R, especially right before a new release.
>
>Many thanks,
>Jenny
>
>At 11:57 AM 9/11/2007, Seth Falcon wrote:
> >Hi Jenny,
> >
> >Jenny Drnevich <drnevich at uiuc.edu> writes:
> > > I posted this message last week, but didn't get any responses. I've
> > > been trying everything I can think of to remove this one problematic
> > > GO term from my HyperGResult object so I can get the other 45
> > > overrepresented GO terms, but I'm not having any luck. I would
> > > appreciate any suggestions!!!
> >
> >Sorry, things have been a bit busy around here :-)
> >
> > > At 12:22 PM 9/5/2007, Jenny Drnevich wrote:
> > >>Hi everyone,
> > >>
> > >>I'm doing hypergeometric testing of GO terms using GOstats on some
> > >>data from ath1121501 Affy arrays. I had some trouble figuring out how
> > >>to work with these arrays at first because the annotation package
> > >>doesn't include EntrezIDs, but after searching the archives I found
> > >>all you had to do was this to get it to work:
> > >>
> > >>ath1121501ENTREZID <- ath1121501ACCNUM
> > >>
> > >>Anyway, everything was going fine, expect in one my HyperGResult
> > >>objects there is a significant GO term that throws up an error:
> > >>
> > >>  >SVC.up.BP <- new("GOHyperGParams", geneIds =
> > >>entrezUniverse.sortVctrl[EID.sortVctrl==1],
> > >>                  universeGeneIds = entrezUniverse.sortVctrl,
> > >>annotation = "ath1121501",
> > >>                  ontology = "BP", pvalueCutoff = hgCutoff,
> > >> conditional = FALSE,
> > >>                  testDirection = "over")
> > >>
> > >>  >SVC.up.BP.results <- hyperGTest(SVC.up.BP)
> > >>
> > >>  >summary(SVC.up.BP.results)
> > >>Error in .checkKeys(value, Lkeys(x), x at ifnotfound) :
> > >>    invalid key "GO:0002226"
> >
> >First, can you try updating your packages.  We've very recently pushed
> >out new candidates for annotation as well as some bug fixes for
> >AnnotationDbi.
> >
> >If the problem persists, can you send me (off-list) an rda file
> >containing your SVC.up.BP object?
> >
> >+ seth
> >
> >--
> >Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center
> >BioC: http://bioconductor.org/
> >Blog: http://userprimary.net/user/
>
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