[BioC] working with two factors in DESeq to analyze RNA-seq

[Gordon K Smyth]

Dear Fernando,

If you're willing read yet another vignette, Section 11 of the edgeR 
vignette

http://bioconductor.org/packages/2.7/bioc/vignettes/edgeR/inst/doc/edgeR.pdf

gives a case study explaining how to do exactly what you ask, comparing 
two groups while accounting for a second factor.  You can include any 
number of factors, test for interactions, and so on.

Best wishes
Gordon

> Date: Tue, 8 Feb 2011 11:02:35 -0600
> From: "Biase, Fernando" <biase at illinois.edu>
> To: "bioconductor at r-project.org" <bioconductor at r-project.org>
> Subject: [BioC] working with two factors in DESeq to analyze RNA-seq
>
> Dear Dr Anders,
>
> Based on my readings I am willing to use DESeq to analyze my RNA-seq 
> data. I found it very easy to follow your instructions written on the 
> package vignette, and to work with it for one factor comparison. 
> However, I am not sure if I am using it correctly to account for a 
> second factor in the model. So, here are my two questions:
>
> How do I compare two groups, accounting for a second factor in the 
> model?  (it is not a factorial model that I am looking for)
>
> Can I simply write:
> The condition  names as
> "Ax", "Ax", "Ax", "Ax", "Ay", "Ay", "Ay", "Bx", "Bx", "Bx", "By", "By", "By"
>
> nbinomTest ( cds, "A", "B")
>
> being A/B may main factor and x/y my secondary factor?
>
> That is what I understood from the page 3 of the vignette
>
> "> conds <- c( "T", "T", "T", "Tb", "N", "N" )
> where \T" stands for a sample derived from a certain tumour type and \N" for a sample derived
> from non-pathological tissue. The
> rst three samples had a very similar histopathological phe-
> notype, while the fourth sample was atypical, and hence, we assign it another condition (\Tb").
> "
>
> Can I test for interaction effect between two factors?
>
> Thanks so much,
> Fernando
>
> Research Associate - PhD
> -----------------------------------------------------------------------
> University of Illinois at Urbana-Champaign
> Institute for Genomic Biology
> Principal Investigator: Prof Dr Harris Lewin
>
> 210 Edward R. Madigan Laboratory
> 1201 W. Gregory Drive
> Urbana, IL 61801
> Phone: (217) 244-6745 E-mail: biase at illinois.edu
> -----------------------------------------------------------------------

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