[BioC] HuGene as exon array

[cstrato]

Dear Tim,

Thank you very much for testing the new version. I am glad to hear that 
it works for you.

Best regards
Christian


Tim Rayner wrote:
> Hi Christian,
>
> Thanks very much indeed. I can confirm that xps 1.2.6 certainly works
> as advertised, and produces output comparable with what I've been
> getting with APT. I'll let you know if I encounter any problems, but
> so far I've not found any!
>
> Cheers,
>
> Tim
>
> 2009/2/24 cstrato <cstrato at aon.at>:
>   
>> Dear Tim,
>>
>> I am glad to inform you that a new version of xps is now available from BioC
>> (xps_1.2.6 and xps_1.3.6), and I would very  much appreciate if you could
>> test the new version.
>>
>> Please note that release 4 (r4) of the HuGene array converts it to an exon
>> array, so you need to create the scheme as follows:
>>
>> xps.scheme <-
>> import.exon.scheme("Scheme_HuGene10stv1r4_na27_2",filedir=scmdir,
>>
>> layoutfile=paste(libdir,"HuGene-1_0-st-v1.r4.analysis-lib-files/HuGene-1_0-st-v1.r4.clf",sep="/"),
>>
>> schemefile=paste(libdir,"HuGene-1_0-st-v1.r4.analysis-lib-files/HuGene-1_0-st-v1.r4.pgf",sep="/"),
>>
>> probeset=paste(anndir,"Version09Feb/HuGene-1_0-st-v1.na27.2.hg18.probeset.csv",sep="/"),
>>
>> transcript=paste(anndir,"Version09Feb/HuGene-1_0-st-v1.na27.hg18.transcript.csv",sep="/"))
>>
>>
>> If you summarize the data on the transcript level you should get identical
>> results as before:
>>
>> xps.rma <- rma(xps.cel, "HuGeneMixRMAcore", background="antigenomic",
>>              option="transcript", exonlevel="core+affx")
>>
>>
>> In addition, you can now summarize the data on the probeset (exon) level:
>>
>> xps.rma.ps <- rma(xps.cel, "HuGeneMixRMAcorePS", background="antigenomic",
>>                 option="probeset", exonlevel="core+affx")
>>
>>
>> Please let me know if the new version works as expected.
>>
>> Best regards
>> Christian
>>
>>
>> Tim Rayner wrote:
>>     
>>> Dear Christian,
>>>
>>> Thank you very much for your help - reverting to the older r3 files
>>> does indeed solve the problem. I'll look forward to hearing about the
>>> new version of the xps package, and I'd be more than happy to help
>>> test it if needed.
>>>
>>> Best regards,
>>>
>>> Tim
>>>
>>> 2009/2/17 cstrato <cstrato at aon.at>:
>>>