[BioC] problem with pd.huex.1.0.st.v2 and oligo::getProbeInfo

[Mikhail Pachkov]

Thanks! It worked!

Best regards,

Mikhail

On Thu, Feb 14, 2013 at 3:35 PM, Benilton Carvalho
<beniltoncarvalho at gmail.com> wrote:
> getProbeInfo() has an argument called 'target', which (for Exon/Gene
> ST arrays) is set by default to 'core'.
>
> Looks like you want to add this argument and set it to 'probeset'.
>
> probeInfo <- getProbeInfo(rawdata, c('fid', 'fsetid', 'atom',
> 'transcript_cluster_id','exon_id'), target='probeset')
>
> Best wishes, b
>
> 2013/2/14 Mikhail Pachkov <pachkov at gmail.com>:
>> Dear All,
>>
>> I have got a strange problem. I try to get probe information
>> (particularly I am interested in fsetid, fid, atom) with getProbeInfo
>> function. Here is example:
>>
>> library(oligo);
>> rawdata=read.celfiles("GSM529785.CEL.gz");
>> probeInfo <- getProbeInfo(rawdata, c('fid', 'fsetid', 'atom',
>> 'transcript_cluster_id','exon_id'));
>>
>> However it looks like instead of fsetid function returns transcript_cluster_id:
>>
>>>probeInfo[1,]
>>   fid man_fsetid  fsetid    atom transcript_cluster_id   exon
>> 1  15    3029030 3029030 5132751               3029030 444853
>>
>> If I check directly underlying database
>> pd.huex.1.0.st.v2/extdata/pd.huex.1.0.st.v2.sqlite I can see that
>> function returned transcript_cluster_id instead of fsetid.
>>
>>>select * from pmfeature where atom=5132751;
>> fid|fsetid      | atom     | x | y
>> 15|3029044|5132751|14|0
>>
>> sqlite> select * from featureSet where fsetid=3029044;
>> fsetid|strand|start|stop|transcript_cluster_id|exon_id|crosshyb_type|level|chrom|type
>> 3029044|0|142991717|142991843|3029030|444853|1|1|9|1
>>
>> Do I use wrong arguments for getProbeInfo? Is it bug?
>>
>> Thank you in advance!
>>
>> Best regards,
>>
>> Mikhail Pachkov
>>
>> _______________________________________________
>> 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