[BioC] a warining from edgeR

[Gordon K Smyth]

It would appear that one gene out of 54374 has received a dispersion 
estimate that has not fully converged.  That is very unlikely to affect 
your overall results.

In the devel version of edgeR, to become the release version in October, 
this warning will no longer occur, because we now compute the maximum of 
the spline interpolant exactly.

Best wishes
Gordon

> Date: Sun, 29 Jul 2012 11:13:06 -0400
> From: wang peter <wng.peter at gmail.com>
> To: bioconductor at r-project.org
> Subject: [BioC] a warining from edgeR
>
> I have 35 samples and 54374 genes
>
> such is the coding, do  u think is it ok?
>
>
>
> #normalization
> dge <- calcNormFactors(dge)
>
> treatment=factor(c(rep('control',6),rep('treated',24),rep('control',5)))
> time=factor(c('0h','0h','0h','24h','24h','24h','0h','0h','0h','6h','6h','6h','6h','12h','12h','12h','12h','18h','18h','18h','18h',
>             '24h','24h','24h','36h','36h','36h','48h','48h','48h','6h','12h','18h','36h','48h'))
> design <- model.matrix(~treatment*time)
>
> dge <- estimateGLMCommonDisp(dge, design)
> dge <- estimateGLMTagwiseDisp(dge, design)
>
>
>
> Warning message:
> In maximizeInterpolant(spline.pts, apl.smooth[j, ]) :
>  max iterations exceeded
>
>
>
>
>
>> sessionInfo()
> R version 2.15.1 (2012-06-22)
> Platform: x86_64-pc-mingw32/x64 (64-bit)
>
> locale:
> [1] LC_COLLATE=Chinese (Simplified)_People's Republic of China.936
> [2] LC_CTYPE=Chinese (Simplified)_People's Republic of China.936
> [3] LC_MONETARY=Chinese (Simplified)_People's Republic of China.936
> [4] LC_NUMERIC=C
> [5] LC_TIME=Chinese (Simplified)_People's Republic of China.936
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] edgeR_2.4.6  limma_3.10.3
>
>
> -- 
> shan gao
> Room 231(Dr.Fei lab)
> Boyce Thompson Institute
> Cornell University
> Tower Road, Ithaca, NY 14853-1801
> Office phone: 1-607-254-1267(day)
> Official email:sg839 at cornell.edu
> Facebook:http://www.facebook.com/profile.php?id=100001986532253
>

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