[BioC] DEXSeq package: Error in DEXSeqHTML

[Alejandro Reyes]

Dear Ahmet,

It depends on the R version you are using, 1.0.2 is the release for the 
R version you are using (2.14.2), if you update your R to a newest 
version and install it again via "biocLite", it will install the newest 
version of DEXSeq.

Best wishes,
Alejandro

> oh, I just typed this:
>
>
> source("http://bioconductor.org/biocLite.R")
>      biocLite("DEXSeq")
>
> It installed 1.0.2 again. I'll download the updated version and install
> it manually but something might be broken there. (I check for package
> updates frequently and DEXSeq never updated there either)
>
>
> Ahmet
> On Tue, Jun 5, 2012 at 9:39 AM, Ahmet ZEHIR <ahmetzehir at gmail.com
> <mailto:ahmetzehir at gmail.com>> wrote:
>
>     Dear Alejandro,
>
>     I think back in the day I installed DEXSeq through NCI's mirror and
>     it seems like the package is not updated there. I'm assuming that's
>     why I missed the updates (here 1.0.2 is cited as the current
>     version:
>     http://watson.nci.nih.gov/bioc_mirror/packages/2.9/bioc/html/DEXSeq.html)
>
>     I will update to 1.2 right away. Thanks for your reply!
>
>     Cheers,
>
>     Ahmet Z.
>
>
>     On Tue, Jun 5, 2012 at 4:17 AM, Alejandro Reyes
>     <alejandro.reyes at embl.de <mailto:alejandro.reyes at embl.de>> wrote:
>
>         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
>
>
>
>
>
>     --
>     /Ahmet Z./
>
>
>
>
> --
> /Ahmet Z./