Hello Wolfgang,

In your previous reply you mentioned that I "do the 6 MA -plots for all pairs of samples and where the hits are in there."  According to the DESeq documentation, an MA plot was done after we get the foldchange using the nbinomTest. However, do you suggest trying MA plots using the normalized counts of all 4 samples or do you mean something else when you mentioned looking at the MA plots.

Also, I tried calling 'arrayQualityMetrics' on the variance-stabilized version with both the 'maximum' and 'fit-only' options. However, in both cases I get the following error :

Error in function (classes, fdef, mtable)  :
  unable to find an inherited method for function "platformspecific", for signature "matrix"

I have never used arrayQualityMetrics, but even after looking at the function I couldn't quite understand what might be causing this error. Any help on this would be greatly appreciated.

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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