[BioC] edgeR: Contrast selection

Thomas J Hardcastle tjh48 at cam.ac.uk
Fri Dec 18 17:11:16 CET 2009


http://www.bioconductor.org/packages/release/bioc/vignettes/baySeq/inst/doc/baySeq.pdf

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
>> >
>> > _______________________________________________
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>> > https://stat.ethz.ch/mailman/listinfo/bioconductor
>> > Search the archives:
>> > http://news.gmane.org/gmane.science.biology.informatics.conductor
>> >
>>
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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)
> University Park, PA 16802-2111
>


-- 
Dr. Thomas J. Hardcastle

Department of Plant Sciences
University of Cambridge
Downing Street
Cambridge, CB2 3EA
United Kingdom



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