[BioC] edgeR: Contrast selection

[Martin Morgan]

Thomas J Hardcastle wrote:
> http://www.bioconductor.org/packages/release/bioc/vignettes/baySeq/inst/doc/baySeq.pdf

Hmm, but a little more interesting than that...

The 'build report' for baySeq in the release branch

http://bioconductor.org/checkResults/2.5/bioc-LATEST/

shows a warning on the windows build machine (liverpool) related to the
vignette not being built, and in fact the 'zip' file used to install on
Windows does not contain the pdf.

This is likely an issue on our build machines here in Seattle, so we'll
try and fix this over the next several days.

Martin

> 
> 
> Best,
> 
> Tom
> 
> Naomi Altman wrote:
>> 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
>>> >
>>> > _______________________________________________
>>> > Bioconductor mailing list
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>>> > http://news.gmane.org/gmane.science.biology.informatics.conductor
>>> >
>>>
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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)
>> University Park, PA 16802-2111
>>
> 
> 


-- 
Martin Morgan
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