[BioC] edgeR, glmLRT error

[Cei Abreu-Goodger]

Hi guys,

Many thanks for the update, I'll check the devel in a few weeks.

Best,

Cei

On 7/16/12 11:35 PM, Gordon K Smyth wrote:
> Dear Cei,
>
> Thanks for the nice reproducible example.
>
> We have been working on a programming solution to eliminate this
> occasionally occuring error in edgeR.  We have a nearly complete
> solution in our local (non-public) version of edgeR.  Running your data
> example with our current local code, glmLRT no longer gives an error,
> but the 9th row of your data generates a NA value for the likelihood
> ratio test statistic.
>
> That's already an improvement, but I want to eliminate the NA fits as
> well if possible.
>
> We will push this code out to Bioc-devel soon, but probably not before
> the Bioconductor conference next week.
>
> Best wishes
> Gordon
>
>> Date: Sun, 15 Jul 2012 18:36:16 -0500
>> From: Cei Abreu-Goodger <cei at langebio.cinvestav.mx>
>> To: bioconductor at r-project.org
>> Subject: [BioC] edgeR, glmLRT error
>>
>> Hi Gordon,
>>
>> I've been getting the following error upon running glmLRT:
>>
>> Error in beta[k, ] <- betaj[decr, ]
>>   NAs are not allowed in subscripted assignments
>>
>> which has previously been reported, for instance:
>>
>> https://stat.ethz.ch/pipermail/bioconductor/2011-February/038079.html
>>
>> I subsetted my count data (originally ~14k rows) to narrow down the
>> culprit row, and I would like to send you this example in case it can be
>> used to improve the glm fitting code. If it turns out to be impossible
>> to completely avoid these kinds of errors, perhaps it would be nice to
>> return the genes that are generating the NAs so that we can more easily
>> remove them and proceed?
>>
>> I can also avoid this particular case by using only the CommonDisp or
>> heavily increasing the prior.n, but that kind of defeats the purpose of
>> the TagwiseDisp.
>>
>> Example code and sessionInfo:
>>
>> ################
>> library(edgeR)
>>
>> counts <-
>> read.table("http://datos.langebio.cinvestav.mx/~cei/counts.tab")
>> grp <- sub("_R.+", "", colnames(counts))
>> dge <- DGEList(counts=counts, group=grp)
>> dge <- calcNormFactors(dge)
>>
>> design <- model.matrix(~0 + dge$samples$group)
>> colnames(design) <- levels(dge$samples$group)
>>
>> dge <- estimateGLMCommonDisp(dge, design)
>> dge <- estimateGLMTagwiseDisp(dge, design)
>>
>> fit <- glmFit(dge, design)
>> lrt <- glmLRT(dge, fit, contrast=c(0,0,0,-1,0.5,0.5))
>>
>> Error in beta[k, ] <- betaj[decr, ] :
>>   NAs are not allowed in subscripted assignments
>>
>> ################
>> R version 2.15.0 (2012-03-30)
>> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
>>
>> locale:
>> [1] C/UTF-8/C/C/C/C
>>
>> attached base packages:
>> [1] grDevices datasets  stats     graphics  utils     methods   base
>>
>> other attached packages:
>> [1] edgeR_2.6.9         limma_3.12.1        Biobase_2.16.0
>> BiocGenerics_0.2.0  BiocInstaller_1.4.7
>>
>> ################
>>
>>
>> Many thanks,
>>
>> Cei
>>
>> --
>> Dr. Cei Abreu-Goodger
>> Langebio CINVESTAV
>> Tel: (52) 462 166 3006
>> cei at langebio.cinvestav.mx
>>
>
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