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

[Gordon K Smyth]

Hi Laurent,

Could you possibly send me a data example?

Regards
Gordon

On Mon, 3 Jan 2011, Laurent Gautier wrote:

> 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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