[BioC] DEXSeq package: Error in DEXSeqHTML

[Alejandro Reyes]

Dear Ahmet,

Thanks for your report!
You are using a quite old version of DEXSeq (1.0.2), I would recommend 
you try updating to one of the most recent versions, both in the current 
stable or the current devel this should not be a problem any more.Let me 
know if its not the case.

Best wishes,
Alejandro


> Dear list,
>
> I am using DEXseq to look at differential exon usage and everything seems
> to work just fine. When I want to create an HTML report however, I get the
> following error:
>
>> DEXSeqHTML(ecsA673vshMSC, FDR = 0.001, color = c("#FF000080",
> "#0000FF80"))
> Error in plot.new() : figure margins too large
> In addition: Warning message:
> In plotDEXSeq(ecs, geneID = gene, FDR = FDR, lwd = 2, expression = opts[1],
>   :
>    This gene contains more than 42 transcripts annotated, only the first 42
> will be plotted
>
> After this error, the function quits and the output is not complete. Is
> there a way to turn this message off and continue outputting the rest of
> the HTML report?
>
> Thanks,
>
>> sessionInfo()
> R version 2.14.2 (2012-02-29)
> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
>
> locale:
> [1] C/en_US.UTF-8/C/C/C/C
>
> attached base packages:
> [1] grDevices datasets  splines   graphics  utils     grid      stats
> methods   base
>
> other attached packages:
>   [1] edgeR_2.4.6        limma_3.10.3       biomaRt_2.10.0     DEXSeq_1.0.2
>        Biobase_2.14.0     plyr_1.7.1         reshape2_1.2.1
>   [8] survival_2.36-14   RSQLite_0.11.1     DBI_0.2-5          knitr_0.5
>       gplots_2.10.1      KernSmooth_2.23-7  caTools_1.12
> [15] bitops_1.0-4.1     gdata_2.8.2        gtools_2.6.2
> RColorBrewer_1.0-5 ggplot2_0.9.1
>
> loaded via a namespace (and not attached):
>   [1] MASS_7.3-18      RCurl_1.91-1     Rcpp_0.9.10      XML_3.9-4
>   codetools_0.2-8  colorspace_1.1-1 dichromat_1.2-4  digest_0.5.2
>   [9] evaluate_0.4.2   formatR_0.4      highlight_0.3.1  hwriter_1.3
>   labeling_0.1     memoise_0.1      munsell_0.3      parser_0.0-14
> [17] proto_0.3-9.2    scales_0.2.1     statmod_1.4.14   stringr_0.6
>   tools_2.14.2
>