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

[Benilton Carvalho]

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
>
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