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

[Mª José Nueda]

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,

María 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



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