[BioC] edgeR, error in estimateCommonDisp

[Gordon K Smyth]

Dear Lucia,

This is a failure in the edgeR function estimatePs(), and it is something 
that I have never seen before.

Have you checked that your input counts are as you expect?  For example,

   summary(y$counts)

You don't say what version of edgeR you are using.  Could you please try 
installing the devel version of edgeR, and tell me whether the problem has 
gone away?

Best wishes
Gordon

PS. See the advice about sessionInfo() in the posting guide:

  http://www.bioconductor.org/help/mailing-list/posting-guide/


> Date: Mon, 30 Jul 2012 14:17:31 -0400
> From: Lucia Peixoto <luciap at iscb.org>
> To: bioconductor at r-project.org
> Subject: [BioC]  edgeR, error in estimateCommonDisp
>
> Hi All,
> I am pretty new to edgeR, this is the first time I use the package, as
> well as the first time I try to find differential expression using RNA-Seq
> data (this is the first time I have biological replicates).
> I apologize in advance for my lack of knowledge.
>
> I have 10 samples, 5 biological replicates of each condition, and I am just
> trying to define differentially expressed genes between the two conditions
> I have a matrix of counts in tab delimited format, in which the first
> column is the GeneID and the first row is a header detailing the samples
> this is my code:
>
>> x <- read.delim("RNAseq_AllgenesFCHC_Counts.txt",row.names="GeneID",
> header=TRUE)
>> group <- factor(c(1,1,1,1,1,2,2,2,2,2))
>> y <- DGEList(counts=x,group=group)
>> y <- estimateCommonDisp(y)
>
> and I get the following error:
> Error in if (mx < tol) { : missing value where TRUE/FALSE needed
>
> can anyone explain to me what the error means?
>
> Thank you very much for your help
> Lucia

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