LumiBatch: problem when renaming samples

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Cei Abreu-Goodger ▴ 830

@cei-abreu-goodger-4433

Last seen 9.8 years ago

Mexico

Hi all, this seems like a bug to me, but please correct me if I'm doing something wrong. If I rename the samples of a LumiBatch object, I can no longer subset them by name (with numbers it still works). Here's an example, followed by my sessionInfo. library(lumi) data(example.lumi) # This works example.lumi[,sampleNames(example.lumi)] # But if I rename the samples sampleNames(example.lumi) <- gsub("0","",sampleNames(example.lumi)) # It no longer works example.lumi[,sampleNames(example.lumi)] #Error in example.lumi[, sampleNames(example.lumi)] : # subscript out of bounds ================================================== > sessionInfo() R version 2.7.0 (2008-04-22) i386-apple-darwin8.10.1 locale: C attached base packages: [1] stats graphics grDevices datasets tools utils methods [8] base other attached packages: [1] lumi_1.6.0 mgcv_1.3-30 affy_1.18.0 [4] preprocessCore_1.2.0 affyio_1.8.0 Biobase_2.0.0 -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE.

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ADD COMMENT • link updated 16.7 years ago by Wolfgang Huber ★ 13k • written 16.7 years ago by Cei Abreu-Goodger ▴ 830

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Wolfgang Huber ★ 13k

@wolfgang-huber-3550

Last seen 4 months ago

EMBL European Molecular Biology Laborat…

Dear Cei, Pan, thanks for reporting this. It appears indeed that it is a bug in the lumi package: the "LumiBatch" class inherits from Biobase's "eSet", but has additional slots, and one of the ugly effects is that the sampleNames are stored in multiple places. However, the "sampleNames<-" method is inherited from eSet without modification, so only updates those two places where they are in any eSet, but not the other, LumiBatch-specific occurences, leaving the object in an inconsistent state, which confuses the (LumiBatch- specific) "["-method. Best wishes Wolfgang ------------------------------------------------------------------ Wolfgang Huber EBI/EMBL Cambridge UK http://www.ebi.ac.uk/huber Cei Abreu-Goodger a ?crit 05/05/2008 18:10: > > Hi all, this seems like a bug to me, but please correct me if I'm doing > something wrong. If I rename the samples of a LumiBatch object, I can no > longer subset them by name (with numbers it still works). Here's an > example, followed by my sessionInfo. > > library(lumi) > data(example.lumi) > > # This works > example.lumi[,sampleNames(example.lumi)] > > # But if I rename the samples > sampleNames(example.lumi) <- gsub("0","",sampleNames(example.lumi)) > > # It no longer works > example.lumi[,sampleNames(example.lumi)] > > #Error in example.lumi[, sampleNames(example.lumi)] : > # subscript out of bounds > > > ================================================== >> sessionInfo() > R version 2.7.0 (2008-04-22) > i386-apple-darwin8.10.1 > > locale: > C > > attached base packages: > [1] stats graphics grDevices datasets tools utils methods > [8] base > > other attached packages: > [1] lumi_1.6.0 mgcv_1.3-30 affy_1.18.0 > [4] preprocessCore_1.2.0 affyio_1.8.0 Biobase_2.0.0 > >

ADD COMMENT • link 16.7 years ago Wolfgang Huber ★ 13k

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Hi Cei, Thanks for reporting the bug. As Wolfgang mentioned, we just used the default "sampleNames<-", as a result, some of the colnames of additional elements were not changed. I have updated the code. The updated version is 1.7.2, which should be available in the next few days. Thanks! Pan On 5/6/08 7:43 AM, "Wolfgang Huber" <huber at="" ebi.ac.uk=""> wrote: > Dear Cei, Pan, > > thanks for reporting this. It appears indeed that it is a bug in the > lumi package: the "LumiBatch" class inherits from Biobase's "eSet", but > has additional slots, and one of the ugly effects is that the > sampleNames are stored in multiple places. > > However, the "sampleNames<-" method is inherited from eSet without > modification, so only updates those two places where they are in any > eSet, but not the other, LumiBatch-specific occurences, leaving the > object in an inconsistent state, which confuses the (LumiBatch- specific) > "["-method. > > Best wishes > Wolfgang > > > ------------------------------------------------------------------ > Wolfgang Huber EBI/EMBL Cambridge UK http://www.ebi.ac.uk/huber > > > Cei Abreu-Goodger a ?crit 05/05/2008 18:10: >> >> Hi all, this seems like a bug to me, but please correct me if I'm doing >> something wrong. If I rename the samples of a LumiBatch object, I can no >> longer subset them by name (with numbers it still works). Here's an >> example, followed by my sessionInfo. >> >> library(lumi) >> data(example.lumi) >> >> # This works >> example.lumi[,sampleNames(example.lumi)] >> >> # But if I rename the samples >> sampleNames(example.lumi) <- gsub("0","",sampleNames(example.lumi)) >> >> # It no longer works >> example.lumi[,sampleNames(example.lumi)] >> >> #Error in example.lumi[, sampleNames(example.lumi)] : >> # subscript out of bounds >> >> >> ================================================== >>> sessionInfo() >> R version 2.7.0 (2008-04-22) >> i386-apple-darwin8.10.1 >> >> locale: >> C >> >> attached base packages: >> [1] stats graphics grDevices datasets tools utils methods >> [8] base >> >> other attached packages: >> [1] lumi_1.6.0 mgcv_1.3-30 affy_1.18.0 >> [4] preprocessCore_1.2.0 affyio_1.8.0 Biobase_2.0.0 >> >> >

ADD REPLY • link 16.7 years ago Pan Du ★ 1.2k

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I am trying to use rma or vsn on PM arrays (in particular Mouse 430). Both stoped with an "error in .local(object,...) : subscript out of bounds". (mmindex returns 0 for all probes. Is this the right coding for PM arrays or this is the problem?). Thanks for any help. Roumyana

ADD REPLY • link 16.7 years ago Roumyana Yordanova ▴ 110

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Roumyana Yordanova wrote: > I am trying to use rma or vsn on PM arrays (in particular Mouse 430). > Both stoped with an "error in .local(object,...) : subscript out of > bounds". > (mmindex returns 0 for all probes. Is this the right coding for PM > arrays or this is the problem?). > Thanks for any help. > > Roumyana Dear Roumyana, please send a reproducible example (R script, using data that we can access as well), the output of sessionInfo() and the exact error message you get. Then I or someone might be able to help. Best wishes Wolfgang ------------------------------------------------------------------ Wolfgang Huber EBI/EMBL Cambridge UK http://www.ebi.ac.uk/huber

ADD REPLY • link 16.7 years ago Wolfgang Huber ★ 13k

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Unfortunately the data are confidential so I can not send an example. Actually, the problem is in the summarization. Both vsn2 and rma work for the background and normalziation part but failed for the median polish algorithm. I can do all the steps separately (using pmindex in the last part to do the summary only for pm) and then everything works. Is there any opiton in rma (vsn) that specify use pm only for the summary, i.e. skip an estimation of mm(x). Actually the last command gives the error. Thanks. Roumyana Wolfgang Huber wrote: > Roumyana Yordanova wrote: > >> I am trying to use rma or vsn on PM arrays (in particular Mouse 430). >> Both stoped with an "error in .local(object,...) : subscript out of >> bounds". >> (mmindex returns 0 for all probes. Is this the right coding for PM >> arrays or this is the problem?). >> Thanks for any help. >> >> Roumyana > > > > Dear Roumyana, > > please send a reproducible example (R script, using data that we can > access as well), the output of sessionInfo() and the exact error > message you get. Then I or someone might be able to help. > > Best wishes > Wolfgang > > ------------------------------------------------------------------ > Wolfgang Huber EBI/EMBL Cambridge UK http://www.ebi.ac.uk/huber >

ADD REPLY • link 16.7 years ago Roumyana Yordanova ▴ 110

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> Unfortunately the data are confidential so I can not send an example. If the output of "sessionInfo()" on your end, as well as a copy/paste of the error message thrown by R, are classified it is harder for people to try providing help. > Actually, the problem is in the summarization. Both vsn2 and rma work > for the background and normalziation part but failed for the median > polish algorithm. > I can do all the steps separately (using pmindex in the last part to do > the summary only for pm) and then everything works. > > Is there any opiton in rma (vsn) that specify use pm only for the > summary, i.e. skip an estimation of mm(x). Actually the last command > gives the error. > Thanks. > > Roumyana > > > Wolfgang Huber wrote: > >> Roumyana Yordanova wrote: >> >>> I am trying to use rma or vsn on PM arrays (in particular Mouse 430). >>> Both stoped with an "error in .local(object,...) : subscript out of >>> bounds". >>> (mmindex returns 0 for all probes. Is this the right coding for PM >>> arrays or this is the problem?). >>> Thanks for any help. >>> >>> Roumyana >> >> >> >> Dear Roumyana, >> >> please send a reproducible example (R script, using data that we can >> access as well), the output of sessionInfo() and the exact error >> message you get. Then I or someone might be able to help. >> >> Best wishes >> Wolfgang >> >> ------------------------------------------------------------------ >> Wolfgang Huber EBI/EMBL Cambridge UK http://www.ebi.ac.uk/huber >> > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor >

ADD REPLY • link 16.7 years ago lgautier@altern.org ▴ 950

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This seems to be an issue with the way AffyBatch object is created. The error is: >library(htmg430pmcdf) >data <-ReadAffy(filenames=dir()) >data AffyBatch object size of arrays=744x744 features (14 kb) cdf=HT_MG-430_PM (45163 affyids) number of samples=6 number of genes=45163 annotation=htmg430pm notes= > mm(data) Error in .local(object, ...) : subscript out of bounds In addition: Warning message: NAs introduced by coercion in: .local(object, ...) >mmIndex(data) ------ $`1428469_PM_a_at` [1] 0 0 0 0 0 0 0 0 0 0 0 $`1428470_PM_at` [1] 0 0 0 0 0 0 0 0 0 0 0 $`1428471_PM_at` [1] 0 0 0 0 0 0 0 0 0 0 0 $`1428472_PM_at` [1] 0 0 0 0 0 0 0 0 0 0 0 $`1428473_PM_at` [1] 0 0 0 0 0 0 0 0 0 0 $`1428474_PM_at` [1] 0 0 0 0 0 -------- I am not sure what is the proper coding for mm indexes in a case of PM arrays. Is there an option in ReadAffy that should be used for PM arrays? If this can be fixed then rma and justvsn should work. Thanks. Roumyana >> Unfortunately the data are confidential so I can not send an example. >> > > If the output of "sessionInfo()" on your end, > as well as a copy/paste of the error message thrown by R, > are classified it is harder for people to try providing help. > > > >> Actually, the problem is in the summarization. Both vsn2 and rma work >> for the background and normalziation part but failed for the median >> polish algorithm. >> I can do all the steps separately (using pmindex in the last part to do >> the summary only for pm) and then everything works. >> >> Is there any opiton in rma (vsn) that specify use pm only for the >> summary, i.e. skip an estimation of mm(x). Actually the last command >> gives the error. >> Thanks. >> >> Roumyana >> >> >> Wolfgang Huber wrote: >> >> >>> Roumyana Yordanova wrote: >>> >>> >>>> I am trying to use rma or vsn on PM arrays (in particular Mouse 430). >>>> Both stoped with an "error in .local(object,...) : subscript out of >>>> bounds". >>>> (mmindex returns 0 for all probes. Is this the right coding for PM >>>> arrays or this is the problem?). >>>> Thanks for any help. >>>> >>>> Roumyana >>>> >>> Dear Roumyana, >>> >>> please send a reproducible example (R script, using data that we can >>> access as well), the output of sessionInfo() and the exact error >>> message you get. Then I or someone might be able to help. >>> >>> Best wishes >>> Wolfgang >>> >>> ------------------------------------------------------------------ >>> Wolfgang Huber EBI/EMBL Cambridge UK http://www.ebi.ac.uk/huber >>> >>> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> >> > > > > [[alternative HTML version deleted]]

ADD REPLY • link 16.7 years ago Roumyana Yordanova ▴ 110

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