Dear Wolfgang,

Thank you very much for your reply. I understand that I need to validate my results if I make any changes, but was not clear as to how would I do that. I like the idea of using the MA plots and am currently working on those.

However, I would like your suggestion on what you think could be better in our case to identify anything as potentially differentially expressed. Should I just go with the defaults (which I think might be too conservative specifically for our condition), or should I make certain changes.

I have already tried all the possible changes in parameters for estimatDispersions, and definitely see different results than default. I am currently validating all these changes, but would just like an expert view on what would be a good modification to default (if any).

Kind regards,
Praful

Praful Aggarwal
Broeckel Lab
Human and Molecular Genetics Center
Medical College of Wisconsin
8701 Watertown Plank Road
CRI/TBRC 2nd Floor
Milwaukee, WI 53226

414-955-2567


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