[BioC] exporting mas5 data with xps

[cstrato]

Dear Addiel,

The output shows you that "UnitName" shows the probeset ID and 
"ProbesetID" shows the transcript ID. So you are right.

BTW, I do not see your sessionInfo().
The reason I am asking is that looking at the source code of my current 
version I realized that I have already replaced "ProbesetID" with 
"TranscriptID" to avoid confusion.

Best regards
Christian


On 2/1/11 1:37 AM, Addiel de Alba wrote:
> cstrato<cstrato at ...>  writes:
>
>>
>> Dear Addiel,
>>
>> Yes, it is the transcript_cluster_id in the Affymetrix annotation,
>> assuming that you have used mas5(...,option = "transcript",..). If you
>> have used mas5(...,option = "probeset",..) then it will be the
>> probeset_id, see ?mas5.
>>
>> BTW, can you please always supply your sessionInfo().
>>
>> Best regards
>> Christian
>>
>> On 1/30/11 12:28 AM, Addiel U. de Alba Solis wrote:
>>>
>>> Dear Christian,
>>>
>>> I am following the script4exon you provide to process HuEx-1_0-st-v2 data.
>>> When exporting after processing and making MAS5 calls:
>>>
>>>> export.expr(data.x.mas5,
>>> varlist="fUnitName:fTranscriptID",outfile="MAS5EXPRLEVELS.txt")
>>>
>>> The command replies with:
>>>
>>> NULL , and then exports the text file
>>>
>>> However instead of having a transcript ID field(label) it has a ProbesetID
>>> field. Is this the transcript ID?
>>>
>>> Also a general question. Is your transcript ID referring to the
>>> transcript_cluster_id in affymetrix annotation?
>>>
>>> Best regards,
>>>
>>> Addiel de Alba
>>>
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>>
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>
> Dear Christian,
>
> First I am using the probeset option with mas5
> to generate expression levels:
>
>> data.x.mas5.ps<-
> mas5(data.exon,"MixExonMAS5MetacorePS",
> filedir=datdir,tmpdir="",normalize=TRUE,sc=500,option="
> probeset",exonlevel="metacore", update=TRUE)
>
> And then I am exporting with:
>
>> export.expr(data.x.mas5.ps,outfile="CEMMAS5EXPLEVELPS.txt")
>
> The output file shows the next fields:
>
> UNIT_ID	UnitName	ProbesetID	GeneName  .....
> 392	2315588	2315554	NM_001130045
> 393	2315589	2315554	NM_001130045
> 395	2315591	2315554	NM_001130045
> 398	2315594	2315554	NM_001130045
> 399	2315595	2315554	NM_001130045
> 400	2315596	2315554	NM_001130045
> ....
>
> Then I am using the transcript option while doing mas5 to
> generate expression levels:
>
> data.x.mas5<-
> mas5(data.exon,"MixExonMAS5MetacoreAll",
> filedir=datdir,tmpdir="",normalize=TRUE,sc=500,option="t
> ranscript",exonlevel="metacore", update=TRUE)
>
> And then I am exporting with:
>
>> export.expr(data.x.mas5,outfile="CEMMAS5EXPLEVELTR.txt")
>
> The output file shows the next fields:
>
> UNIT_ID	UnitName	ProbesetID ...	
> 153	2315554	2315554	
> 157	2315633	2315633	
> 170	2315674	2315674	
> 174	2315739	2315739	
> 212	2315894	2315894	
> .....
>
> So from what you are saying even when the field says ProbesetID
> it actually contains the Trascript ID in
> both cases. Is that right?
>
> Below I included my sessionInfo()
>
> Best,
>
> Addiel
>
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