[BioC] edgeR: Contrast selection

[Naomi Altman]

I just installed baySeq.  Most of the documentation is there, but I 
cannot find the vignette.

--Naomi


At 04:38 AM 12/18/2009, Krys Kelly wrote:
>Hi Simon,
>
>You could try Tom Hardcastle's baySeq package which allows more complex
>designs.  There isn't an example of a three group design in the vignette,
>but there is one in the draft manuscript which we are about to send off.
>Perhaps Tom might email you a copy of this example.
>
>Cheers
>
>Krys
>
>
>Dr Krystyna A Kelly (Krys)
>Bioinformatics Group Leader
>
>Department of Plant Sciences
>University of Cambridge
>Downing Street
>Cambridge CB2 3EA
>United Kingdom
>
>Tel: +44 (0)1223 748 969
>Fax: +44 (0)1223 333 953
>
>
>
>-----Original Message-----
>From: bioconductor-bounces at stat.math.ethz.ch
>[mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Sunny
>Srivastava
>Sent: 17 December 2009 23:59
>To: Simon Anders
>Cc: BioC list
>Subject: Re: [BioC] edgeR: Contrast selection
>
>Dear Simon,
>The last time I used edgeR, it was only supported 2 groups comparisons. As
>you have three treatment groups, this may be a possible problem.
>
>It may be a bug, but it may be also related to the limitation of this
>package.
>
>Hope this helps!
>
>Mark, pls correct me if I am wrong.
>
>Thanks and Best Regards,
>S.
>
>On Wed, Dec 16, 2009 at 1:03 PM, Simon Anders <anders at embl.de> wrote:
>
> > Dear Mark
> >
> > I cannot figure out how to specify which conditions to contrast against
> > each other in an edgeR exactTest.
> >
> > I do the following:
> >
> > > library( edgeR )
> > > counts <- matrix( rnbinom( 600, 5, .1 ), ncol=6 )
> > > conds <- c( "A", "A", "B", "B", "C", "C" )
> > > dgl <- DGEList( counts=counts, group=conds )
> > Warning message:
> > In DGEList(counts = counts, group = conds) :
> >  Calculating library sizes from total number of reads for each library.
> > > dgl <- estimateCommonDisp( dgl )
> >
> > Now I have a DGEList with 6 samples in 3 conditions. If I want to contrast
> > 'C' vs 'A', I assume I should do
> >
> > > res <- exactTest( dgl, c( "A", "C" ) )
> >
> > However, I get this error here:
> >
> > Comparison of groups:  C - A
> > Error in Ops.factor(pair[1], group) : level sets of factors are different
> >
> >
> > Have I misunderstood the syntax, or is this a bug? I've tried around a bit
> > with passing a factor instead, even with all three levels, but this did
>not
> > help.
> >
> > Thanks in advance for any help.
> >
> > Cheers
> >  Simon
> >
> >
> > > sessionInfo()
> > R version 2.11.0 Under development (unstable) (--)
> > x86_64-unknown-linux-gnu
> >
> > locale:
> >  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
> >  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
> >  [5] LC_MONETARY=C              LC_MESSAGES=en_US.UTF-8
> >  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
> >  [9] LC_ADDRESS=C               LC_TELEPHONE=C
> > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
> >
> > attached base packages:
> > [1] stats     graphics  grDevices utils     datasets  methods   base
> >
> > other attached packages:
> > [1] edgeR_1.5.3
> >
> > loaded via a namespace (and not attached):
> > [1] limma_3.3.1
> >
> >
> >
> > +---
> > | Dr. Simon Anders, Dipl.-Phys.
> > | European Molecular Biology Laboratory (EMBL), Heidelberg
> > | office phone +49-6221-387-8632
> > | preferred (permanent) e-mail: sanders at fs.tum.de
> >
> > _______________________________________________
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> >
>
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Naomi S. Altman                                814-865-3791 (voice)
Associate Professor
Dept. of Statistics                              814-863-7114 (fax)
Penn State University                         814-865-1348 (Statistics)
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