[BioC] hgu133plus2GENENAME and topTable

[James W. MacDonald]

Lance Palmer wrote:
> 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.

How about (untested):

names <- sapply(mget(ids, hgu133plus2GENENAME), function(x) x[1])
## you could use unlist here, but if there are multiple genenames then
## the length of 'names' would be too long
my.table <- data.frame("Names" = names, tt)

HTH,

Jim


> 
>  
> 
> 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")
> 
> 
> 	[[alternative HTML version deleted]]
> 
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-- 
James W. MacDonald
University of Michigan
Affymetrix and cDNA Microarray Core
1500 E Medical Center Drive
Ann Arbor MI 48109
734-647-5623



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