[BioC] exporting mas5 data with xps

[Addiel de Alba]

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