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.

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. > ______________________________________________________________________ The information in this email is confidential and intend...{{dropped:4}}