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@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@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.*

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