Selecting of most differentially expressed transcripts

Question

[Valentina]

Hello all,

I did Differential Expression Analysis (using edgeR in Blast2GO Pro) for two groups at four different treatment time points, now I have to select most 25 differentially expressed transcripts (up and down regulated) for each time point for both groups and then I have to compare them but I don't know how to do that. I have to select them based on fold change.

Thanks in advance :)

[Valentina]

Thank you very much Devon! Do you know is it any possible way to do that in Blast2GO because later I want to compare the most DE transcripts between two groups based on GO ID.

[GenoMax]

Please use ADD COMMENT/ADD REPLY when responding to existing posts to keep threads logically organized.

[Devon Ryan]

I suspect that you'll need to prefilter the input into Blast2GO, but I can't say for sure (I don't normally have any need for Blast2GO).

Answer 1

[Devon Ryan]

First filter by adjusted p-value and then sort by the absolute value of the fold change. You can even do that in eXcel if you really want...