[BioC] DESeq estimateDispersion options for lower depth

[Wolfgang Huber]

Dear Praful

thanks. One thing to remember is that DESeq does not do magic. It will 
only find what is in the data. A well-designed, sufficiently powered and 
carefully executed experiment is worth a lot.

	best wishes
	Wolfgang


Mar/27/12 9:55 PM, Aggarwal, Praful scripsit::
> 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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>
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> fig:phenotypiclandscape}



-- 
Best wishes
	Wolfgang

Wolfgang Huber
EMBL
http://www.embl.de/research/units/genome_biology/huber