Entering edit mode
Dear Fernando,
I can guess what the problem is and, if I'm right, it is a bug and you
haven't done anything wrong. The TrendedDisp function is separating
your
observations into bins based on average expression (essentially total
read
count), then passing each bin to dispCoxReid(). However dispCoxReid()
by
default ignores all transcripts with total counts less than 5. I
suspect
that the first bin of your data is made up entirely of transcripts
with
total counts less than 5, leading dispCoxReid() to filter all the
available observations and hence to give an error.
I will consult with the edgeR team here to get this bug fixed. In the
meantime, my guess is that everything will work for you perfectly if
you
remove rows with total count less than 5. None of these transcripts
can
possibly give significant differences in any case.
A <- rowSums(getCounts(eset_a_tmm))
eset_a_tmm <- eset_a_tmm[A>=5,]
etc.
Best wishes
Gordon
> Date: Fri, 29 Apr 2011 11:46:05 -0500
> From: "Biase, Fernando" <biase at="" illinois.edu="">
> To: "bioconductor at r-project.org" <bioconductor at="" r-project.org="">
> Subject: [BioC] problems with estimateGLMTrendedDisp()
> Content-Type: text/plain
>
> Dear list members,
>
> I am having problems using the function estimateGLMTrendedDisp() in
> edgeR. When I run it on my dataset, it returns the error:
>
> eset_b_tmm <- estimateGLMTrendedDisp(eset_a_tmm , design)
>
> Error in dispCoxReid(y, design, offset = offset, ...) :
> no data rows with required number of counts
>
> If I run the estimateGLMCommonDisp() function in my dataset it
works.
>
> If I run the example from the Documentation page it works. I have
read
> the documentation but I do not find the source of my problem.
>
> My object eset_a_tmm is a "DGEList".
>
> The only difference I see between my dataset and the y from the
> Documentation page is that my data has samples and some genes with 0
> (zero) counts.
>
> Does anyone have a clue of what I am doing wrong?
>
> Thanks very much,
> Fernando
>
> sessionInfo()
> R version 2.13.0 (2011-04-13)
> Platform: x86_64-pc-mingw32/x64 (64-bit)
>
> locale:
> [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United
States.1252
> [3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C
> [5] LC_TIME=English_United States.1252
>
> attached base packages:
> [1] splines stats graphics grDevices utils datasets
methods base
>
> other attached packages:
> [1] DESeq_1.4.0 locfit_1.5-6 lattice_0.19-23 akima_0.5-4
Biobase_2.12.0
> [6] edgeR_2.2.1
>
> loaded via a namespace (and not attached):
> [1] annotate_1.30.0 AnnotationDbi_1.14.0 DBI_0.2-5
> [4] genefilter_1.34.0 geneplotter_1.30.0 grid_2.13.0
> [7] limma_3.8.0 RColorBrewer_1.0-2 RSQLite_0.9-4
> [10] survival_2.36-5 tools_2.13.0 xtable_1.5-6
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