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@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@fs.tum.de
>
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