Getting the actually expression values in a DEG analysis

Question

[hakimelakhrass]

Hello,

When doing a differentially expressed genes analysis in limma and using the toptables() function to get the results you do not get the actually expression level changes, just the fold change. Is there anyway to get the actually expression level change? Thanks.

[Sean Davis]

What do you mean by "expression level change"?

[hakimelakhrass]

I mean the actual gene expression value at each time point (in my case) for th DEG.

[ivivek_ngs]

are you referring to the normalized expression values for your samples? then upon normalization you can put the normalized values to a vector which can be saved as a matrix and should be giving you the desired output you are asking for. This is what I can make from your question

[hakimelakhrass]

That would be for all genes yes but I want the expression levels of the confirmed differentially expressed genes. So like I said when you use toptable you get the genes, the fold change between experiments, p value etc... But not the actually expression level at each condition (time in my case)

[ivivek_ngs]

In any case if you create the expression matrix which are basically normalized value of the genes across samples, either RPKM(single-end) , FPKM (paired-end) or TPM , then you will have so called expression values for all genes across all samples. Once you have the list of DEGs you can use this list to fetch the expression values of all the DEGs acorss all your samples that groups the DE analysis samples. This is a very straight-forward approach used for heatmap generation as well.

[hakimelakhrass]

Sorry I should mention I am using microarrays. I assume to what you are saying you should use some sort of shell script to match your DEG to you normalized list? Do you know of a way to do it automatically through limma?