[BioC] Is there any prejudice whether to use edgeR or DESeq for differential expression analysis for RNA Seq data

[Nicolas Delhomme]

Hi all,

There are some information about performing diff. exp. analysis after aligning with RSEM on the RSEM webpage: http://deweylab.biostat.wisc.edu/rsem/README.html#de. Using EBSeq, a (non yet Bioc as far as I can tell) R package.

Depending on how you ran RSEM - see there for RSEM output details: http://deweylab.biostat.wisc.edu/rsem/rsem-calculate-expression.html - you'll get TPM or FPKM values that are not suitable for being used with edgeR/DESeq. 

But an interesting proxy for counts might be the "expected_count" column of the result file, i.e. count corrected for multiple mapping. Comparing the outcome of edgeR/DESeq using these and the result you'd obtain from EBSeq is certainly worth a try.

HTH,

Nico

---------------------------------------------------------------
Nicolas Delhomme

Nathaniel Street Lab
Department of Plant Physiology
Umeå Plant Science Center

Tel: +46 90 786 7989
Email: nicolas.delhomme at plantphys.umu.se
SLU - Umeå universitet
Umeå S-901 87 Sweden
---------------------------------------------------------------

On Nov 7, 2012, at 3:58 PM, Steve Lianoglou wrote:

> Hi,
> 
> On Wed, Nov 7, 2012 at 9:42 AM, Sakshi Gulati
> <Sakshi.Gulati at cancer.org.uk> wrote:
>> Hi Mark,
>> 
>> Thanks for answering. It makes more sense now. I have upper quartile normalised RSEM counts per gene. Is that ok as an input for edgeR and/or DESeq?
> 
> My guess is that they are not fine.
> 
> Not familiar with RSEM, but if these are actually *counts* (first hint
> that they are not counts if they are not integers) then you are ok. If
> these are something like (R|F)PKM, then you're not -- ditto if you are
> already inputting numbers that have been previously scaled to library
> size.
> 
> -steve
> 
> -- 
> Steve Lianoglou
> Graduate Student: Computational Systems Biology
> | Memorial Sloan-Kettering Cancer Center
> | Weill Medical College of Cornell University
> Contact Info: http://cbio.mskcc.org/~lianos/contact
> 
> _______________________________________________
> 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