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 [[alternative HTML version deleted]]

Dear Praful On 3/29/12 8:00 PM, Aggarwal, Praful wrote: > 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. Yes, you can do several things: 1. A = average expression over all six samples and M=log fold change between sum of the counts within groups 2. Each pairwise MA-plot I was thinking of 2. I think what you refer to in the documentation is 1. > 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. Sorry. Indeed this requires some programming on my end to make it convenient. I'll implement this asap and will announce it here. Until then, if you are suffciently familiar with Bioconductor data structures, what needs to be done is to create an ExpressionSet which contains the data matrix, and whose featureData and phenoData are taken from the countDataSet. This is explained in the vignette of the package Biobase "An introduction to Biobase and ExpressionSets". Best wishes Wolfgang > 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 > > > [[alternative HTML version deleted]] > > _______________________________________________ Bioconductor mailing > list Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor Search the > archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor -- Best wishes Wolfgang Wolfgang Huber EMBL http://www.embl.de/research/units/genome_biology/huber