exporting mas5 data with xps

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Addiel de Alba ▴ 30

@addiel-de-alba-4457

Last seen 9.6 years ago

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 > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor at ... > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > > > > _______________________________________________ > Bioconductor mailing list > Bioconductor at ... > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > > 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.exprdata.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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ADD COMMENT • link updated 13.2 years ago by cstrato ★ 3.9k • written 13.2 years ago by Addiel de Alba ▴ 30

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cstrato ★ 3.9k

@cstrato-908

Last seen 5.6 years ago

Austria

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 >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor at ... >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >>> >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at ... >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >> >> > > 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.exprdata.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 > > _______________________________________________ > 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 >

ADD COMMENT • link 13.2 years ago cstrato ★ 3.9k

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