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

kristen.dang at syngenta.com kristen.dang at syngenta.com
Wed Dec 29 21:39:01 CET 2010

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

> traceback()
3: mglmOneGroup(y, offset, dispersion)
2: adjustedProfileLik(spline.disp[i], y.filt, design = design, offset = offset.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:

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

message may contain confidential information. If you are not the designated recipient, please notify the sender immediately, and delete the original and any copies. Any use of the message by you is prohibited. 

More information about the Bioc-sig-sequencing mailing list