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Old 03-03-2014, 11:19 AM   #6
Location: St. Louis, MO

Join Date: Apr 2013
Posts: 17

Michael, I was hoping you might be able to answer one more related question...

I've decided that I need to control for batch variation since some of the parasites I'm studying were derived from different host animals at different times of year, etc. I still want to generate a list of genes whose expression varies from stage to stage -- I just want to disregard variation due to other factors as best I can.

Would changing this:
dds <- DESeq(dds, test="LRT", full=~stage, reduced=~1)

to this:
dds <- DESeq(dds, test="LRT", full=~Stage+Date, reduced=~Date)

accomplish my goal? I wanted to double check that I'm not making the reverse comparison and accidentally measuring variation due to collection date.

Also, would you expect to see more DE genes controlling for batch variation or less? I seem to be finding more, and that surprised me (which is what inspired this post -- I'm nearly certain that I'm doing something wrong). I figured that some of the variation I was seeing before was likely due to differences in season or host animal and that pulling those factors out would reduce my DE gene count.
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