[BioC] goSeq error (steve Shen)

[Alicia Oshlack]

Hi Steve,

So it works OK if you use the more accurate "Sampling" method but not if you
use the approximation. It's not clear to me why it's not working for the
down category but does the pwf look ok when you generate it? Are there many
genes DE for the down list?

Cheers,
Alicia



> Message: 1
> Date: Sun, 30 Oct 2011 18:10:51 -0400
> From: steve Shen <shen.sq at gmail.com>
> To: "bioconductor at r-project.org" <bioconductor at r-project.org>
> Subject: [BioC] goSeq error
> Message-ID:
> <CAGvvF4jWnrTbW9H5JgwJ_f4+xEhY7jf_5S_YOVvoNm3c3Mmg2Q at mail.gmail.com>
> Content-Type: text/plain
> 
> Hi All,
> 
> Using goSeq to analyze two gene lists - up regulated and down regulated
> genes generated with edgeR, the up regulated list seems good, but there is
> an error with down regulated list. Couldn't figure out what's wrong with
> it. Please refer to the command line and output below. Thanks very for me
> for help.
> 
> Steve
> 
> # up list
>> lateTrans524up.pwf <- nullp(lateTrans524.up.vector,
> bias.data=hs.glen.assayed, plot.fit=FALSE)
>> lateTrans524up.goWall <- goseq(lateTrans524up.pwf, gene2cat=hs.go,
> test.cats=c("GO:CC", "GO:BP", "GO:MF"))
> Using manually entered categories.
> Calculating the p-values...
>> head(lateTrans524up.goWall)
> 
>> lateTrans524up.goSamp <- goseq(lateTrans524up.pwf, gene2cat=hs.go,
> method="Sampling", repcnt=1000)
> Using manually entered categories.
> Running the simulation...
> Calculating the p-values...
> 100 %   g the p-values...
>> head(lateTrans524up.goSamp)
> 
> # down list
>> lateTrans524dn.pwf <- nullp(lateTrans524.dn.vector,
> bias.data=hs.glen.assayed, plot.fit=FALSE)
>> lateTrans524dn.goWall <- goseq(lateTrans524dn.pwf, gene2cat=hs.go,
> test.cats=c("GO:CC", "GO:BP", "GO:MF"))
> Using manually entered categories.
> Calculating the p-values...
> Error in dWNCHypergeo(subcount, totcount, N - totcount, n, weight) :
>   Invalid value for odds
> 
>> lateTrans524dn.goSamp <- goseq(lateTrans524dn.pwf, gene2cat=hs.go,
> method="Sampling", repcnt=1000)
> Using manually entered categories.
> Running the simulation...
> Calculating the p-values...
> 100 %   g the p-values...
>> head(lateTrans524dn.goSamp)
> 
>> sessionInfo()
> R version 2.12.1 (2010-12-16)
> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
> 
> locale:
> [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
> 
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
> 
> other attached packages:
> [1] GO.db_2.4.5            RSQLite_0.9-4          DBI_0.2-5
> AnnotationDbi_1.12.0   Biobase_2.10.0         edgeR_2.0.5
> [7] goseq_1.2.0            geneLenDataBase_0.99.5 BiasedUrn_1.03
> 
> loaded via a namespace (and not attached):
>  [1] Biostrings_2.18.4   BSgenome_1.18.3     GenomicRanges_1.2.3
> grid_2.12.1         IRanges_1.8.9       lattice_0.19-30
> limma_3.6.9
>  [8] Matrix_0.999375-50  mgcv_1.7-6          nlme_3.1-98
> RCurl_1.6-6         rtracklayer_1.10.6  tools_2.12.1        XML_3.2-0
> 
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> 


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