[BioC] Dexseq package: dexseq_count error message and warnings

[Alejandro Reyes]

Dear Capricy Gao,

You have a very old version of R. If you are installing DEXSeq using the 
function "biocLite", you will have to update your R version at least to 
the latest release.

Bests,
Alejandro

> Oh, you are right. Here is the my session information.
>
> ---------------
> > sessionInfo()R version 2.15.2 (2012-10-26)
> Platform: x86_64-pc-linux-gnu (64-bit)
> other attached packages:
> [1] edgeR_3.0.8        limma_3.14.4       DEXSeq_1.4.0 Biobase_2.16.0
> [5] BiocGenerics_0.4.0
> -------------------
>
> But I downloaded it yesterday...
>
> How should I change it?
>
> And do you have any idea about my warning messages?
>
> Thanks a lot for your help:)
>
>
>
>
>
> On Thursday, November 7, 2013 12:43 AM, Alejandro Reyes 
> <alejandro.reyes at embl.de> wrote:
> Dear Capricy Gao,
>
> Let me know if I am wrong, but it sounds like you are using a vignette 
> found by google that does not match with the version of DEXSeq that 
> you are using.  What version of DEXSeq do you have installed?
>
> The "-r" option was included from DEXSeq 1.7.8, so first make sure 
> that you have this or a newer version installed.
>
> Best regards,
> Alejandro
>
>
>> I am planning to compare the exon usage between samples. This is my first time to use Dexdeq. The problem came when I tried to use dexseq_count.py.
>>
>>
>> My RNAseq data was mapped using tophat, then  the bam file was samtools sorted with -n (by name) , samtools converted the sorted bam into sam
>>
>> I followed the online manual (http://www.bioconductor.org/packages/2.13/bioc/vignettes/DEXSeq/inst/doc/DEXSeq.pdf) to fun dexseq_count:
>>
>> /R/x86_64-pc-linux-gnu-library/2.15/DEXSeq/python_scripts/dexseq_count.py  -r name -p yes -s no HTseqFormat_flatterned.gff sample.sam sample.exonCounts
>>
>>
>> the first error message was :  no such option: -r
>>
>> Could anybody let me know why? On page 5 of the manual, it clearly says this option should be included
>>
>>
>> I then deleted this option and a lot of warnings came out:  claims to have an aligned mate which could not be found. (Is the SAM file properly sorted?)
>>
>> These warnings might came up because when I ran tophat, I did not specify the correct " expected (mean) inner distance between mate pairs". I wonder if I could just remove -p option and treat the file like non paired-end data?
>>
>>
>> Thanks a lot:)
>>
>> 	[[alternative HTML version deleted]]
>>
>>
>>
>> _______________________________________________
>> Bioconductor mailing list
>> Bioconductor at r-project.org  <mailto:Bioconductor at r-project.org>
>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>> Search the archives:http://news.gmane.org/gmane.science.biology.informatics.conductor
>
>
>