[BioC] Error while executing estimateCommonDisp

[Gordon K Smyth]

Dear Surjyendu Ray,

Please upgrade to the new Bioconductor release:

   http://www.bioconductor.org/news/bioc_2_11_release

The function estimatePs() was pretty reliable, but is no longer used in 
the edgeR package in the current release.

Best wishes
Gordon

> Date: Thu,  4 Oct 2012 01:31:01 -0700 (PDT)
> From: "Surjyendu Ray [guest]" <guest at bioconductor.org>
> To: bioconductor at r-project.org, surjray at gmail.com
> Subject: [BioC] Error while executing estimateCommonDisp
>
>
> Dear all,
>         I have a data set where there are two samples, each with four replicates. I have created a DGEList object with the relevant count data. While executing the command:
> estimateCommonDisp(Massed_Spaced_Isoform.DGEList, rowsum.filter = 1)
> I get the following error:
> "Error in if (mx < tol) { : missing value where TRUE/FALSE needed"
> The traceback() output is:
> 3: estimatePs(object, maxr)
> 2: equalizeLibSizes(object, disp = disp, null.hypothesis = FALSE)
> 1: estimateCommonDisp(Massed_Spaced_Isoform.DGEList, rowsum.filter = 1)
>
>      Please advise.
>     Thanking you.
>
> -- output of sessionInfo():
>
> R version 2.15.1 (2012-06-22)
> Platform: x86_64-unknown-linux-gnu (64-bit)
>
> 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=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
> [7] LC_PAPER=C                 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_2.6.10 limma_3.12.1
>
> --
> Sent via the guest posting facility at bioconductor.org.
>

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