[BioC] "topGOdata" object: How to supply gene scores with a predefined list of genes

[Ochsner, Scott A]

Hi,

I would like to attach gene "score" info to a predefined list of
interesting genes to generate a topGOdata object.  The predefined list
of genes was obtained by:
> library(limma)
> library(topGO)
>
input<-cbind(FC=fit$coefficients[,1],pval=p.adjust(fit$p.value[,1],metho
d="BH"))
> selectFUN<-function(x){return(abs(x[,1]) >=1 & x[,2] < 0.05)}
> diffgenes<-selectFUN(input)
> myInterestedGenes<-names(which(diffgenes==T))
> geneNames<-rownames(input)
> geneList<-factor(as.integer(geneNames %in% myInterestedGenes))
> names(geneList)<-geneNames
> str(geneList)
 Factor w/ 2 levels "0","1": 1 1 1 1 1 1 1 1 1 1 ...
 - attr(*, "names")= chr [1:34760] "10338001" "10338003" "10338004"
"10338017" ...

Unfortunately, the predefined list does not contain any DE "score"
information.
I would greatly appreciate any help in attaching the score information
to a predefined list or incorporating p.value as well as fold change
cutoffs into a geneSel function when creating a topGOdata object,

Thanks for any help,

Scott

Scott A. Ochsner, PhD
One Baylor Plaza BCM130, Houston, TX 77030
Voice: (713) 798-6227  Fax: (713) 790-1275

> sessionInfo()
R version 2.9.0 (2009-04-17) 
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] stats     graphics  grDevices utils     datasets  methods   base


other attached packages:
[1] topGO_1.12.0        SparseM_0.80        GO.db_2.2.11
RSQLite_0.7-1       DBI_0.2-4           AnnotationDbi_1.6.1
Biobase_2.4.1       graph_1.22.2        limma_2.18.2       

loaded via a namespace (and not attached):
[1] grid_2.9.0      lattice_0.17-25 tools_2.9.0