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

[Laurent Gautier]

Hi Gordon,

We seem to be experiencing the same issue here, although not originating 
from mglmOneGroup(), and edgeR-2.0.3 does not change the outcome:

> dge_disp <- estimateCRDisp(dge_list, design)
Error in if (any(decr)) { : missing value where TRUE/FALSE needed
> traceback()
3: mglmLS(y, design, dispersion, offset = offset)
2: adjustedProfileLik(spline.disp[i], y.select, design = design,
        offset = offset.mat.select + lib.size.mat.select)
1: estimateCRDisp(dge_list, design)
> sessionInfo()
R version 2.12.1 (2010-12-16)
Platform: x86_64-pc-linux-gnu (64-bit)

locale:
[1] C

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

other attached packages:
[1] edgeR_2.0.3

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



Best,


Laurent



On 1/3/11 4:36 AM, Gordon K Smyth wrote:
> Dear Kirsten,
>
> The error is arising in mglmOneGroup. I have just updated the relevant,
> code in edgeR version 2.0.3. Can you try it and see if you get the same
> error?
>
> With regard to the warning message, I can't think of any reason why
> edgeR would evaluate the Poisson density at a non-integer value if you
> have provided integer values. Have you checked that you have provided
> strictly integer counts? Try
>
> data$counts <- round(data$counts)
> data.cd = estimateCRDisp(data, design)
>
> to see if it makes any difference. If it does, then the data you entered
> are not all integers.
>
> We are planning to revise estimateCRDisp() quite a bit during the next
> month or so.
>
> Best wishes
> Gordon
>
>> Date: Wed, 29 Dec 2010 15:39:01 -0500
>> From: <kristen.dang at syngenta.com>
>> To: <bioc-sig-sequencing at r-project.org>
>> Subject: [Bioc-sig-seq] error msg from edgeR estimateCRDisp
>>
>> 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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