Many thanks Sean. Jing -----Original Message----- From: seandavi@gmail.com [mailto:seandavi@gmail.com] On Behalf Of Sean Davis Sent: Thursday, March 22, 2012 4:29 AM To: Jing Huang Cc: bioconductor at r-project.org Subject: Re: [BioC] eset from GEOqury pkg On Wed, Mar 21, 2012 at 6:43 PM, Jing Huang <huangji at="" ohsu.edu=""> wrote: > Hi Sean, > > Do you know that eset generated from GDS dataset a few month ago is different from the eset generated now? Thanks, Jing, for the bug report. This is fixed in 2.20.9 and 2.21.9 (release and devel) and should be available in a day or two. Sean > Old eset: > >> eset > ExpressionSet (storageMode: lockedEnvironment) > assayData: 22690 features, 5 samples > ?element names: exprs > protocolData: none > phenoData > ?sampleNames: GSM60394 GSM60393 ... GSM60391 (5 total) > ?varLabels: sample protocol disease.state description > ?varMetadata: labelDescription > featureData > ?featureNames: 1415670_at 1415671_at ... AFFX-TrpnX-M_at (22690 total) > ?fvarLabels: ID Gene.title ... GO.Component.1 (21 total) > ?fvarMetadata: Column labelDescription > experimentData: use 'experimentData(object)' > Annotation: > > > New eset: > >> eset > ExpressionSet (storageMode: lockedEnvironment) > assayData: 22690 features, 5 samples > ?element names: exprs > protocolData: none > phenoData > ?sampleNames: GSM60394 GSM60393 ... GSM60391 (5 total) > ?varLabels: sample protocol disease.state description > ?varMetadata: labelDescription > featureData > ?featureNames: 1415670_at 1415671_at ... AFFX-TrpnX-M_at (22690 total) > ?fvarLabels: 1 2 ... 21 (21 total) > ?fvarMetadata: Column labelDescription > experimentData: use 'experimentData(object)' > Annotation: > > The difference is in ?fvarLabels. > > Could you advise? How to get these names back? > > Jing > > OHSU > > > ? ? ? ?[[alternative HTML version deleted]] > > _______________________________________________ > 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

Hi, I should rectify that I used the GSE approach (ie getGEO("GSE2773")) and everything is fine whereas I have just checked again using the GDS approach (ie x = getGEO("GDS2248"); y = GDS2eSet(x)) and it does indeed return just numbered fvarLabels as you stated. Best. J. On 22/03/12 09:45, James F. Reid wrote: > Hi, > > I cannot replicate this with the current version of R/BioC and with the > devel one (to be released very soon), i.e I always get the fvarLabels > (like in your 'old' scenario). > You didn't provide a sessionInfo() so I do not know what you are using > and cannot help more. > > J. > > On 21/03/12 22:43, Jing Huang wrote: >> Hi Sean, >> >> Do you know that eset generated from GDS dataset a few month ago is >> different from the eset generated now? >> >> Old eset: >> >>> eset >> ExpressionSet (storageMode: lockedEnvironment) >> assayData: 22690 features, 5 samples >> element names: exprs >> protocolData: none >> phenoData >> sampleNames: GSM60394 GSM60393 ... GSM60391 (5 total) >> varLabels: sample protocol disease.state description >> varMetadata: labelDescription >> featureData >> featureNames: 1415670_at 1415671_at ... AFFX-TrpnX-M_at (22690 total) >> fvarLabels: ID Gene.title ... GO.Component.1 (21 total) >> fvarMetadata: Column labelDescription >> experimentData: use 'experimentData(object)' >> Annotation: >> >> >> New eset: >> >>> eset >> ExpressionSet (storageMode: lockedEnvironment) >> assayData: 22690 features, 5 samples >> element names: exprs >> protocolData: none >> phenoData >> sampleNames: GSM60394 GSM60393 ... GSM60391 (5 total) >> varLabels: sample protocol disease.state description >> varMetadata: labelDescription >> featureData >> featureNames: 1415670_at 1415671_at ... AFFX-TrpnX-M_at (22690 total) >> fvarLabels: 1 2 ... 21 (21 total) >> fvarMetadata: Column labelDescription >> experimentData: use 'experimentData(object)' >> Annotation: >> >> The difference is in fvarLabels. >> >> Could you advise? How to get these names back? >> >> Jing >> >> OHSU >> >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> 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 >>