I am analyzing some affy data.  I have used limma to generate a list of
differentially expressed genes.

 

 

>From topTable

 

               ID   M   A    t P.Value    B

36593   227337_at 3.0 9.0 15.3   0.032 -1.5

10619 201170_s_at 2.8 7.3 13.5   0.032 -1.6

19183 209774_x_at 3.1 6.7 13.1   0.032 -1.6

13022   203574_at 1.4 5.9 12.8   0.032 -1.6

.

 

I want to associate gene descriptions to the table.

 

If I do

tt<- topTable(eb, coef=1, adjust="fdr")

ids<-tt$ID

library(hgu133plus2)

gn<-as.list(hgu133plus2GENENAME)

top<-gn[ids]

 

 

top just has a list as follows.

 

$"227337_at"

[1] "ankyrin repeat domain 37"

 

$"201170_s_at"

[1] "basic helix-loop-helix domain containing, class B, 2"

 

$"209774_x_at"

[1] "chemokine (C-X-C motif) ligand 2"

 

$"203574_at"

[1] "nuclear factor, interleukin 3 regulated"

 

 

How do I associate the gene names with the topTable output shown above.

Better yet, is there a way to include this information anywhere in the
pipeline so that it is included in the topTable.

(ie before lmFit is utilized)

 

Thanks,

 

Lance Palmer

 

 

PS here is the pipeline I am using

 

targets<-readTargets("targets.txt")

data<-ReadAffy(filenames=targets$filename)

eset<-rma(data)

exp<-targets$Name

design<-model.matrix(~-1+factor(exp))

colnames(design)<-c("SH","FT")

contrast.matrix <- makeContrasts(SH-FT, levels=design)

fit <- lmFit(eset, design)

fit2 <- contrasts.fit(fit, contrast.matrix)

eb <- eBayes(fit2)

topTable(eb, coef=1, adjust="fdr")


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