Dear John,
I'm happy to work with you to solve any programs, but first you need to be
using the current Bioconductor release. Bioconductor 2.11 was released on
3 October 2012, see
http://www.bioconductor.org/news/bioc_2_11_release/
and the current version of edgeR is 3.0.2. There are substantial
differences between the current version and the version you are using.
The type of divergence that is being reported in the warnings is now
impossible.
R has just changed from six monthly releases to annual releases, and
Bioconductor seems to have taken most users by surprise by releasing a new
version of Bioconductor while the version of R remains the same.
Best wishes
Gordon
--------------- original message -----------------
[BioC] edgeR warnings and then error
john herbert arraystruggles at gmail.com
Fri Nov 9 17:22:15 CET 2012
Hello Bioconductors,
For some data, the code below works great and I find differentially
expressed genes. However, I have added some biological replicates to
the data, which caused warnings and then an error.
The warnings come from the estimateGLMTagwiseDisp function, then an
error appears in the glmLRT function.
I tried the development version of R and edgeR but this now is still
running after several days.
In summary, glmLRT works fine if no warnings are produced by
estimateGLMTagwiseDisp as below but with warnings, it breaks down.
There could be a work-around but not seen this yet.
Thank you in advance of any tips.
Kind regards,
John..
> library(edgeR)
>
> group <-
factor(c("c","c","c","c","sp","sp","sp","sp","lp","lp","lp","lp","ss","ss","ss","ss","ls","ls","ls","ls","ag","ag","ag","ag"),
levels=c("c","sp","lp","ss","ls","ag"))
> batch <- factor(c(1,2,3,3,1,2,3,3,1,2,3,3,1,2,3,3,1,2,3,3,1,2,3,3))
> design <- model.matrix(~batch+group)
>
> counts <- read.table("Final_L1_L2_L3_mine_simple_all_reads")
>
> x4=counts
>
> y4 <- DGEList(counts=x4,group=group)
Calculating library sizes from column totals.
>
> y4 <- estimateGLMCommonDisp(y4,design)
>
> y4 <- estimateGLMTrendedDisp(y4,design)
>
> y4 <- estimateGLMTagwiseDisp(y4,design)
There were 24 warnings (use warnings() to see them)
>
> fit4 <- glmFit(y4, design)
>
> lrt4 <- glmLRT(fit4, coef=3)
Error in array(x, c(length(x), 1L), if (!is.null(names(x))) list(names(x),
:
dims [product 0] do not match the length of object [13]
> warnings()
Warning messages:
1: In maximizeInterpolant(spline.pts, apl.smooth[j, ]) : Divergence
2: In maximizeInterpolant(spline.pts, apl.smooth[j, ]) : Divergence
3: In maximizeInterpolant(spline.pts, apl.smooth[j, ]) : Divergence
4: In maximizeInterpolant(spline.pts, apl.smooth[j, ]) : Divergence
5: In maximizeInterpolant(spline.pts, apl.smooth[j, ]) : max iterations
exceeded
6: In maximizeInterpolant(spline.pts, apl.smooth[j, ]) : max iterations
exceeded
7: In maximizeInterpolant(spline.pts, apl.smooth[j, ]) : Divergence
8: In maximizeInterpolant(spline.pts, apl.smooth[j, ]) : Divergence
9: In maximizeInterpolant(spline.pts, apl.smooth[j, ]) : max iterations
exceeded
10: In maximizeInterpolant(spline.pts, apl.smooth[j, ]) : Divergence
11: In maximizeInterpolant(spline.pts, apl.smooth[j, ]) : Divergence
12: In maximizeInterpolant(spline.pts, apl.smooth[j, ]) : Divergence
13: In maximizeInterpolant(spline.pts, apl.smooth[j, ]) : Divergence
14: In maximizeInterpolant(spline.pts, apl.smooth[j, ]) : max
iterations exceeded
15: In maximizeInterpolant(spline.pts, apl.smooth[j, ]) : Divergence
16: In maximizeInterpolant(spline.pts, apl.smooth[j, ]) : Divergence
17: In maximizeInterpolant(spline.pts, apl.smooth[j, ]) : Divergence
18: In maximizeInterpolant(spline.pts, apl.smooth[j, ]) : max
iterations exceeded
19: In maximizeInterpolant(spline.pts, apl.smooth[j, ]) : Divergence
20: In maximizeInterpolant(spline.pts, apl.smooth[j, ]) : Divergence
21: In maximizeInterpolant(spline.pts, apl.smooth[j, ]) : Divergence
22: In maximizeInterpolant(spline.pts, apl.smooth[j, ]) : max
iterations exceeded
23: In maximizeInterpolant(spline.pts, apl.smooth[j, ]) : Divergence
24: In maximizeInterpolant(spline.pts, apl.smooth[j, ]) : max
iterations exceeded
> sessionInfo()
R version 2.15.2 (2012-10-26)
Platform: x86_64-w64-mingw32/x64 (64-bit)
locale:
[1] LC_COLLATE=English_United Kingdom.1252 LC_CTYPE=English_United
Kingdom.1252 LC_MONETARY=English_United Kingdom.1252 LC_NUMERIC=C
[5] LC_TIME=English_United Kingdom.1252
attached base packages:
[1] splines stats graphics grDevices utils datasets
methods base
other attached packages:
[1] pasilla_0.2.13 DEXSeq_1.2.1 DESeq_1.8.3
locfit_1.5-8 edgeR_2.6.12 plyr_1.7.1
genefilter_1.38.0 Biobase_2.16.0
[9] BiocGenerics_0.2.0 limma_3.12.3
loaded via a namespace (and not attached):
[1] annotate_1.34.0 AnnotationDbi_1.18.0 biomaRt_2.12.0
DBI_0.2-5 geneplotter_1.34.0 grid_2.15.2
hwriter_1.3
[8] IRanges_1.14.2 lattice_0.20-10 RColorBrewer_1.0-5
RCurl_1.91-1.1 RSQLite_0.11.1 statmod_1.4.16
stats4_2.15.2
[15] stringr_0.6 survival_2.36-14 tools_2.15.2
XML_3.9-4.1 xtable_1.7-0
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