[BioC] DESeq estimateDispersion options for lower depth miRNA-seq

Wolfgang Huber whuber at embl.de
Thu Mar 29 21:53:23 CEST 2012

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


> 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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Best wishes

Wolfgang Huber

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