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Question: Limma and DEG
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gravatar for mathavanbioinfo
17 months ago by
mathavanbioinfo10 wrote:

hi

I am using LIMMA to identify DEGs. I got the top 5 DEGs. But i am not able to get the whole list of DEGs with proper id and genes. 

Here i used the code 

write.table(topTable(fit, coef=1, adjust="fdr", sort.by="B", number=500), file="limma_complete.xls", row.names=F, sep="\t")

 

ADD COMMENTlink modified 17 months ago by Aaron Lun19k • written 17 months ago by mathavanbioinfo10
1
gravatar for Aaron Lun
17 months ago by
Aaron Lun19k
Cambridge, United Kingdom
Aaron Lun19k wrote:

If you want the entire list of DEGs, set number=Inf.

If you want the gene names in the output, supply a data frame or vector with the relevant information to genelist when calling topTable. Or, store it in fit$genes, as shown in the example below:

fit$genes <- data.frame(GeneId=paste0("Gene", 1:nrow(fit)))
ADD COMMENTlink modified 17 months ago • written 17 months ago by Aaron Lun19k
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