Dear List, I really need help with this. I am in the middle of writing a manuscript and need this data. Basically I have a matrix of counts (data) made up of large counts without decimal points. I also have my edesign object with the Group column filled with all 1's since I am trying to do single series time course analysis. The design matrix and everything turn out fine. However, when I try to use p.vector with counts=TRUE, I get this error: fit=p.vector(data, design, counts=TRUE, min.obs=0) Error in if (model.glm$null.deviance == 0) { : missing value where TRUE/FALSE needed I have tried this so many different ways and cannot figure out how to correct the error. Please help. Audra -- output of sessionInfo(): > sessionInfo() R version 3.0.2 (2013-09-25) Platform: x86_64-apple-darwin10.8.0 (64-bit) locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] tcltk parallel stats graphics grDevices utils datasets methods base other attached packages: [1] maSigPro_1.34.0 DynDoc_1.40.0 widgetTools_1.40.0 MASS_7.3-29 Biobase_2.22.0 [6] BiocGenerics_0.8.0 loaded via a namespace (and not attached): [1] limma_3.18.13 Mfuzz_2.20.0 tkWidgets_1.40.0 tools_3.0.2 -- Sent via the guest posting facility at bioconductor.org.

Hi Audra, This error is due to there are some case with a lot of zeros. Before applying maSigPro, these data must be removed. And remember that data must be normalized. Regards, Mar?a J. Nueda -----Mensaje original----- From: Audra Andrew [guest] Sent: Saturday, March 08, 2014 12:37 AM To: bioconductor at r-project.org ; audra.loy at mavs.uta.edu Subject: [BioC] maSigPro RNAseq data (counts=TRUE will not work for negativebinomial) Dear List, I really need help with this. I am in the middle of writing a manuscript and need this data. Basically I have a matrix of counts (data) made up of large counts without decimal points. I also have my edesign object with the Group column filled with all 1's since I am trying to do single series time course analysis. The design matrix and everything turn out fine. However, when I try to use p.vector with counts=TRUE, I get this error: fit=p.vector(data, design, counts=TRUE, min.obs=0) Error in if (model.glm$null.deviance == 0) { : missing value where TRUE/FALSE needed I have tried this so many different ways and cannot figure out how to correct the error. Please help. Audra -- output of sessionInfo(): > sessionInfo() R version 3.0.2 (2013-09-25) Platform: x86_64-apple-darwin10.8.0 (64-bit) locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] tcltk parallel stats graphics grDevices utils datasets methods base other attached packages: [1] maSigPro_1.34.0 DynDoc_1.40.0 widgetTools_1.40.0 MASS_7.3-29 Biobase_2.22.0 [6] BiocGenerics_0.8.0 loaded via a namespace (and not attached): [1] limma_3.18.13 Mfuzz_2.20.0 tkWidgets_1.40.0 tools_3.0.2 -- Sent via the guest posting facility at bioconductor.org. _______________________________________________ Bioconductor mailing list Bioconductor at r-project.org https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor