[BioC] edgeR warnings and then error

[john herbert]

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