[BioC] maSigPro RNAseq data (counts=TRUE will not work for negative binomial)

Audra Andrew [guest] guest at bioconductor.org
Sat Mar 8 00:37:19 CET 2014

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.


 -- output of sessionInfo(): 

> sessionInfo()
R version 3.0.2 (2013-09-25)
Platform: x86_64-apple-darwin10.8.0 (64-bit)

[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

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