[BioC] edgeR: dispersion estimation

[Gordon K Smyth]

Dear Yanzhu,

Please send me your data offlist so that we can trouble-shoot.

Best wishes
Gordon

> Date: Wed,  7 May 2014 11:29:40 -0700 (PDT)
> From: "Yanzhu [guest]" <guest at bioconductor.org>
> To: bioconductor at r-project.org, mlinyzh at gmail.com
> Subject: [BioC] edgeR: dispersion estimation
>
> Dear Gordon,
>
> Sorry for replying late, I am sick and take some days off. The following are my answers to your questions:
>
> I have checked they are all integers, they are read counts generated by HT-Seq (v0.5.3p9). When I type your command I get zero as below:
>
> max(y$counts-floor(y$counts))
> [1] 0
>
>
> I have also posted the session information as below. Both the R and edgeR package are the most recent versions. However, the results are still the same as before.
>
> Are there other possible reasons that would cause such issue?
>
>
> Thank you very much for your help! I greatly appreciate it.
>
>
>
> Yanzhu
>
>
> ########################################
> Dear Yanzhu,
>
> I find it hard to believe that your data are all integers, because there
> is something seriously wrong, and we have only ever seen the problem you
> report when there are fractional counts.
>
> How have you checked that they are all integers?  How were the counts
> created?  What do you see if you type:
>
>   max(y$counts-floor(y$counts))
>
> It also isn't clear that you have installed the current version of edgeR.
> Have you installed R 3.1.0?  Can you please give the sessionInfo() output?
> The current version of edgeR is 3.6.1, whereas you seem to be using
> version 3.2.4, which is two Bioconductor releases out of date.
>
> Gordon
>
>
>
> -- output of sessionInfo():
>
>> sessionInfo()
> R version 3.1.0 (2014-04-10)
> Platform: x86_64-w64-mingw32/x64 (64-bit)
>
> locale:
> [1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252    LC_MONETARY=English_United States.1252
> [4] LC_NUMERIC=C                           LC_TIME=English_United States.1252
>
> attached base packages:
> [1] parallel  stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] DESeq_1.16.0         lattice_0.20-29      locfit_1.5-9.1       Biobase_2.24.0       BiocGenerics_0.10.0
> [6] edgeR_3.6.1          limma_3.20.1         BiocInstaller_1.14.2
>
> loaded via a namespace (and not attached):
> [1] annotate_1.42.0      AnnotationDbi_1.26.0 DBI_0.2-7            genefilter_1.46.0    geneplotter_1.42.0
> [6] GenomeInfoDb_1.0.2   grid_3.1.0           IRanges_1.22.6       RColorBrewer_1.0-5   RSQLite_0.11.4
> [11] splines_3.1.0        stats4_3.1.0         survival_2.37-7      tools_3.1.0          XML_3.98-1.1
> [16] xtable_1.7-3

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