[Bioc-sig-seq] error msg from edgeR estimateCRDisp

[kristen.dang at syngenta.com]

Dear fellow edgeR users,

I have an RNA-seq dataset with 2 factors and 24 samples (balanced) that I am attempting to analyze with edgeR. I keep encountering the following error when I use the estimateCRDisp function.

> data.cd = estimateCRDisp(data, design)
Error in while (any(i)) { : missing value where TRUE/FALSE needed
In addition: There were 50 or more warnings (use warnings() to see the first 50)
> warnings()
Warning messages:
1: In dpois(y[i, ], lambda = mu[i, ], log = TRUE) : non-integer x = 530.381844
2: In dpois(y[i, ], lambda = mu[i, ], log = TRUE) : non-integer x = 676.500000
[etc]

> traceback()
3: mglmOneGroup(y, offset, dispersion)
2: adjustedProfileLik(spline.disp[i], y.filt, design = design, offset = offset.mat.filt +
       lib.size.mat.filt)
1: estimateCRDisp(data, design)
>

I see why the "dpois" function is giving an error, but I am not sure why a non-integer value is being sent to it. Any suggestions are greatly appreciated.


Information about my session and commands follows:

library(edgeR)
targets = read.csv("design_file.csv")
targets$factor_a = factor(targets$factor_a)
targets$factor_b = factor(targets$factor_b)

data = readDGE(targets)
data = calcNormFactors(data)

contrasts(targets$factor_a) = contr.sum(2)
contrasts(targets$factor_b) = contr.sum(2)
design = model.matrix(~factor_a+factor_b, data = targets)
data.cd = estimateCRDisp(data, design)


> sessionInfo()
R version 2.12.0 (2010-10-15)
Platform: i386-pc-mingw32/i386 (32-bit)

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] edgeR_2.0.2

loaded via a namespace (and not attached):
[1] limma_3.6.9  tools_2.12.0



Kristen Dang, Ph.D.
Computational Biologist
Syngenta Biotechnology
Research Triangle Park, NC




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