differential expression in R

Question

[sam]

Hi, I analyzed RNAseq data to assess differential expression in R and when I opened the final excel file(file downloaded by "write.table" function) containing differential expression data, the first column was supposed to sort by Ensembl ID but instead of that, the data was sorted by row names number(I guess). What should I do?

[ATpoint]

That is limma, is it? Can you show a head() of the topTable output? Are the gene names present in it? You probably need to move the rownames to the object before writing it as a file.

[Friederike]

Seconding this, also: which parameters did you use with the write.table() function?