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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