[BioC] question on easyRNASeq developer version

[Nicolas Delhomme]

Hi René, Yanju,

The bug has been fixed in both release and development. It took longer as first it was a complex one, second it was around the Bioc release time and third another bug appeared in another dependencies while I was testing it.

Concerning the long time to generate the geneModel, I've seen that as well and that is again a behavior that has changed between Bioc 2.10 and 2.11. I'm working on it, thanks for your patience.

Cheers,

Nico

---------------------------------------------------------------
Nicolas Delhomme

Genome Biology Computational Support

European Molecular Biology Laboratory

Tel: +49 6221 387 8310
Email: nicolas.delhomme at embl.de
Meyerhofstrasse 1 - Postfach 10.2209
69102 Heidelberg, Germany
---------------------------------------------------------------





On Sep 28, 2012, at 8:52 AM, René Böttcher wrote:

> Hi Nico,
> 
> That is correct, glad to hear that you already tracked down the bug.
> 
> Kind regards,
> René
> 
>> Hi René,
>> 
>> I suppose that's the email you mentioned would be on hold, right?
>> 
>> Nico
>> 
>> ---------------------------------------------------------------
>> Nicolas Delhomme
>> 
>> Genome Biology Computational Support
>> 
>> European Molecular Biology Laboratory
>> 
>> Tel: +49 6221 387 8310
>> Email: nicolas.delhomme at embl.de
>> Meyerhofstrasse 1 - Postfach 10.2209
>> 69102 Heidelberg, Germany
>> ---------------------------------------------------------------
>> 
>> 
>> 
>> 
>> 
>> On Sep 27, 2012, at 10:51 AM, RenéBöttcher wrote:
>> 
>>>> Dear René,
>>>> 
>>>> The best place to post this - where you would get for sure my attention - is
>>> the bioconductor mailing list. The
>>>> advantage is that other developers/users might be able to help you as your
>>> message would have a better
>>>> visibility to the R/Bioc community. I've actually put that mailing list in Cc.
>>>> 
>>>> There indeed seem to be a sub-setting error somewhere within the function that
>>> parses the read
>>>> information, or so I guess from your error message. Would it be possible for
>>> you to share your
>>>> EMC_18_alignment.bam file? I can set up a folder in my dropbox for you to
>>> upload the file. If that is not
>>>> possible, can you at least trim your bam file to the smallest size sufficient
>>> to reproduce the error and
>>>> share that excerpt with me?
>>>> 
>>>> Best,
>>>> 
>>>> Nico
>>>> 
>>>> ---------------------------------------------------------------
>>>> Nicolas Delhomme
>>>> 
>>>> Genome Biology Computational Support
>>>> 
>>>> European Molecular Biology Laboratory
>>>> 
>>>> Tel: +49 6221 387 8310
>>>> Email: nicolas.delhomme at ...
>>>> Meyerhofstrasse 1 - Postfach 10.2209
>>>> 69102 Heidelberg, Germany
>>>> ---------------------------------------------------------------
>>>> 
>>>> On Sep 20, 2012, at 2:04 PM, René Böttcher wrote:
>>>> 
>>>>> Dear Mr. Delhomme,
>>>>> 
>>>>> I would like to ask for your support concerning a problem I'm facing when
>>> using your easyRNASeq package.
>>>> There seems to be an issue in one of the subfunctions,
>>>>> however, I am not able to tell which one, as the error message is rather
>>> short.
>>>>> "Error in mk_singleBracketReplacementValue(x, value) :
>>>>> 'value' must be a CompressedIntegerList object"
>>>>> 
>>>>> Please not that I'm trying to follow the example cases you provided and I am
>>> currently using the developer
>>>> version since my alignments require multiple reads length support according to
>>> your current stable
>>>> release. You can find a detailed problem description on Seqanswers, as it
>>> seems I am not the only one
>>>> encountering this problem.
>>>>> http://seqanswers.com/forums/showthread.php?t=23477
>>>>> 
>>>>> With kind regards,
>>>>> René Böttcher
>>>> _______________________________________________
>>>> Bioconductor mailing list
>>>> Bioconductor at ...
>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>>>> Search the archives:
>>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>>>> 
>>> 
>>> Dear Nicolas,
>>> 
>>> I ran picard-tools FixMateInformation on my bam-file, however, it did not solve
>>> the problem. Additionally, the problem also occurs with another sample, so I
>>> will now crop both of these bam-files to reduce their size and still retain
>>> reproducibility. If you could provide me with your dropbox folder, I can then
>>> upload them for you to test where the bug occurs.
>>> 
>>> Thank you for your support.
>>> 
>>> With kind regards,
>>> René
>>> 
>>> _______________________________________________
>>> Bioconductor mailing list
>>> Bioconductor at r-project.org
>>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
>