Question: problem with function rma
0
gravatar for julin@aecom.yu.edu
12.5 years ago by
julin@aecom.yu.edu80 wrote:
Hello Bioconductorers, I am working with 12 affy rat2302 chips recently. It was OK when I tried to read my cel files into R: > RatData<-ReadAffy() > list.celfiles() [1] "Rat 16hrs-1-2113.CEL" "Rat 16hrs-2-2114.CEL" "Rat 16hrs-3-2115.CEL" [4] "Rat 30hrs-1-2116.CEL" "Rat 30hrs-2-2117.CEL" "Rat 30hrs-3-2118.CEL" [7] "Rat 4hrs-1-2110.CEL" "Rat 4hrs-2-2111.CEL" "Rat 4hrs-3-2112.CEL" [10] "Rat Normal-1-2107.CEL" "Rat Normal-2-2108.CEL" "Rat Normal-3-2109.CEL" > phenoData(RatData) <- read.phenoData("phenoData.txt",header=T) > show(pData(phenoData(RatData))) ID time replicate Rat Normal-1-2107.CEL 2107 0 1 Rat Normal-2-2108.CEL 2108 0 2 Rat Normal-3-2109.CEL 2109 0 3 Rat 4hrs-1-2110.CEL 2110 4 1 Rat 4hrs-2-2111.CEL 2111 4 2 Rat 4hrs-3-2112.CEL 2112 4 3 Rat 16hrs-1-2113.CEL 2113 16 1 Rat 16hrs-2-2114.CEL 2114 16 2 Rat 16hrs-3-2115.CEL 2115 16 3 Rat 30hrs-1-2116.CEL 2116 30 1 Rat 30hrs-2-2117.CEL 2117 30 2 Rat 30hrs-3-2118.CEL 2118 30 3 However, when I was going to do normalization, I got an error message as following: > esetRat <- rma(RatData) Background correcting Normalizing Calculating Expression Error in validObject(.Object) : invalid class "exprSet" object: sampleNames different from names of phenoData rows Can anyboday give me a clue on how to solve this problem? BTW. my sessionInfor is as following: > sessionInfo() R version 2.4.0 (2006-10-03) i386-pc-mingw32 locale: LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 attached base packages: [1] "splines" "tools" "methods" "stats" "graphics" "grDevices" [7] "utils" "datasets" "base" other attached packages: rat2302cdf affyQCReport simpleaffy genefilter survival affy "1.14.0" "1.12.0" "2.8.0" "1.12.0" "2.31" "1.12.1" affyio Biobase "1.2.0" "1.12.2" Thanks a lot! Juan
ADD COMMENTlink modified 12.5 years ago by Seth Falcon7.4k • written 12.5 years ago by julin@aecom.yu.edu80
Answer: problem with function rma
0
gravatar for Martin Morgan
12.5 years ago by
Martin Morgan ♦♦ 24k
United States
Martin Morgan ♦♦ 24k wrote:
Hi Juan -- "Juan Lin" <julin at="" aecom.yu.edu=""> writes: > Hello Bioconductorers, > > I am working with 12 affy rat2302 chips recently. It was OK when I tried to > read my cel files into R: > >> RatData<-ReadAffy() >> list.celfiles() > [1] "Rat 16hrs-1-2113.CEL" "Rat 16hrs-2-2114.CEL" "Rat 16hrs-3-2115.CEL" > [4] "Rat 30hrs-1-2116.CEL" "Rat 30hrs-2-2117.CEL" "Rat 30hrs-3-2118.CEL" > [7] "Rat 4hrs-1-2110.CEL" "Rat 4hrs-2-2111.CEL" "Rat 4hrs-3-2112.CEL" > [10] "Rat Normal-1-2107.CEL" "Rat Normal-2-2108.CEL" "Rat Normal-3-2109.CEL" > probably sampleNames(RatData) returns the same vector as list.celfiles() ? >> phenoData(RatData) <- read.phenoData("phenoData.txt",header=T) probably validObject(RatData) would fail here -- you're allowed to assign inconsistent names, in the hopes that you're going to make them consistent again in the next line... >> show(pData(phenoData(RatData))) > ID time replicate > Rat Normal-1-2107.CEL 2107 0 1 > Rat Normal-2-2108.CEL 2108 0 2 > Rat Normal-3-2109.CEL 2109 0 3 > Rat 4hrs-1-2110.CEL 2110 4 1 > Rat 4hrs-2-2111.CEL 2111 4 2 > Rat 4hrs-3-2112.CEL 2112 4 3 > Rat 16hrs-1-2113.CEL 2113 16 1 > Rat 16hrs-2-2114.CEL 2114 16 2 > Rat 16hrs-3-2115.CEL 2115 16 3 > Rat 30hrs-1-2116.CEL 2116 30 1 > Rat 30hrs-2-2117.CEL 2117 30 2 > Rat 30hrs-3-2118.CEL 2118 30 3 Notice that the cel files and phenoData names are not in the same order-- you've associated the wrong phenoData with your cel files. One thing you could do is pd <- read.phenoData("phenoData.txt",header=TRUE) pd <- pd[sampleNames(RatData),] # re-order; check carefully phenoData(RatData) <- pd validObject(RatData) > However, when I was going to do normalization, I got an error message as > following: > >> esetRat <- rma(RatData) > Background correcting > Normalizing > Calculating Expression > Error in validObject(.Object) : invalid class "exprSet" object: sampleNames > different from names of phenoData rows > > Can anyboday give me a clue on how to solve this problem? > > BTW. my sessionInfor is as following: R 2.5.0 is out, and so are the 1.14.x series of affy and Biobase. One thing that will change when you update is that affy will produce an eSet-based AffyBatch, which is slightly different: 1) update any old instances with rat <- updateObject(RatData) 2) use read.AnnotatedDataFrame rather than read.phenoData. Hope that helps, Martin >> sessionInfo() > R version 2.4.0 (2006-10-03) > i386-pc-mingw32 > > locale: > LC_COLLATE=English_United States.1252;LC_CTYPE=English_United > States.1252;LC_MONETARY=English_United > States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 > > attached base packages: > [1] "splines" "tools" "methods" "stats" "graphics" "grDevices" > [7] "utils" "datasets" "base" > > other attached packages: > rat2302cdf affyQCReport simpleaffy genefilter survival > affy > "1.14.0" "1.12.0" "2.8.0" "1.12.0" "2.31" > "1.12.1" > affyio Biobase > "1.2.0" "1.12.2" > > Thanks a lot! > Juan > > _______________________________________________ > 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 -- Martin Morgan Bioconductor / Computational Biology http://bioconductor.org
ADD COMMENTlink written 12.5 years ago by Martin Morgan ♦♦ 24k
Martin, It works after I change the order of phenoData names! And I will update both R and bioconductor today. Thanks a lot for your help! Juan -----Original Message----- From: Martin Morgan [mailto:mtmorgan@fhcrc.org] Sent: Tuesday, May 29, 2007 9:27 PM To: Juan Lin Cc: bioconductor at stat.math.ethz.ch Subject: Re: [BioC] problem with function rma Hi Juan -- "Juan Lin" <julin at="" aecom.yu.edu=""> writes: > Hello Bioconductorers, > > I am working with 12 affy rat2302 chips recently. It was OK when I tried to > read my cel files into R: > >> RatData<-ReadAffy() >> list.celfiles() > [1] "Rat 16hrs-1-2113.CEL" "Rat 16hrs-2-2114.CEL" "Rat 16hrs-3-2115.CEL" > [4] "Rat 30hrs-1-2116.CEL" "Rat 30hrs-2-2117.CEL" "Rat 30hrs-3-2118.CEL" > [7] "Rat 4hrs-1-2110.CEL" "Rat 4hrs-2-2111.CEL" "Rat 4hrs-3-2112.CEL" > [10] "Rat Normal-1-2107.CEL" "Rat Normal-2-2108.CEL" "Rat Normal-3-2109.CEL" > probably sampleNames(RatData) returns the same vector as list.celfiles() ? >> phenoData(RatData) <- read.phenoData("phenoData.txt",header=T) probably validObject(RatData) would fail here -- you're allowed to assign inconsistent names, in the hopes that you're going to make them consistent again in the next line... >> show(pData(phenoData(RatData))) > ID time replicate > Rat Normal-1-2107.CEL 2107 0 1 > Rat Normal-2-2108.CEL 2108 0 2 > Rat Normal-3-2109.CEL 2109 0 3 > Rat 4hrs-1-2110.CEL 2110 4 1 > Rat 4hrs-2-2111.CEL 2111 4 2 > Rat 4hrs-3-2112.CEL 2112 4 3 > Rat 16hrs-1-2113.CEL 2113 16 1 > Rat 16hrs-2-2114.CEL 2114 16 2 > Rat 16hrs-3-2115.CEL 2115 16 3 > Rat 30hrs-1-2116.CEL 2116 30 1 > Rat 30hrs-2-2117.CEL 2117 30 2 > Rat 30hrs-3-2118.CEL 2118 30 3 Notice that the cel files and phenoData names are not in the same order-- you've associated the wrong phenoData with your cel files. One thing you could do is pd <- read.phenoData("phenoData.txt",header=TRUE) pd <- pd[sampleNames(RatData),] # re-order; check carefully phenoData(RatData) <- pd validObject(RatData) > However, when I was going to do normalization, I got an error message as > following: > >> esetRat <- rma(RatData) > Background correcting > Normalizing > Calculating Expression > Error in validObject(.Object) : invalid class "exprSet" object: sampleNames > different from names of phenoData rows > > Can anyboday give me a clue on how to solve this problem? > > BTW. my sessionInfor is as following: R 2.5.0 is out, and so are the 1.14.x series of affy and Biobase. One thing that will change when you update is that affy will produce an eSet-based AffyBatch, which is slightly different: 1) update any old instances with rat <- updateObject(RatData) 2) use read.AnnotatedDataFrame rather than read.phenoData. Hope that helps, Martin >> sessionInfo() > R version 2.4.0 (2006-10-03) > i386-pc-mingw32 > > locale: > LC_COLLATE=English_United States.1252;LC_CTYPE=English_United > States.1252;LC_MONETARY=English_United > States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 > > attached base packages: > [1] "splines" "tools" "methods" "stats" "graphics" "grDevices" > [7] "utils" "datasets" "base" > > other attached packages: > rat2302cdf affyQCReport simpleaffy genefilter survival > affy > "1.14.0" "1.12.0" "2.8.0" "1.12.0" "2.31" > "1.12.1" > affyio Biobase > "1.2.0" "1.12.2" > > Thanks a lot! > Juan > > _______________________________________________ > 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 -- Martin Morgan Bioconductor / Computational Biology http://bioconductor.org
ADD REPLYlink written 12.5 years ago by julin@aecom.yu.edu80
Answer: problem with function rma
0
gravatar for Seth Falcon
12.5 years ago by
Seth Falcon7.4k
Seth Falcon7.4k wrote:
Martin Morgan <mtmorgan at="" fhcrc.org=""> writes: > R 2.5.0 is out, and so are the 1.14.x series of affy and Biobase. One > thing that will change when you update is that affy will produce an > eSet-based AffyBatch, which is slightly different: > > 1) update any old instances with rat <- updateObject(RatData) > > 2) use read.AnnotatedDataFrame rather than read.phenoData. > Just to clarify: if you want to upgrade to the latest BioC packages, you need to also upgrade to the latest release of R. Based on your sessionInfo, it looks like you have a mix since you have affy 1.14.0 (part of BioC 2.0 release) and your other packages are part of the 1.9 release and appropriate for your version of R. Did you install via some mechanism other than biocLite? In any case, mixing versions like this is not supported. I would recommend upgrading your R and reinstalling BioC using biocLite. + seth >>> sessionInfo() >> R version 2.4.0 (2006-10-03) >> i386-pc-mingw32 >> >> locale: >> LC_COLLATE=English_United States.1252;LC_CTYPE=English_United >> States.1252;LC_MONETARY=English_United >> States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 >> >> attached base packages: >> [1] "splines" "tools" "methods" "stats" "graphics" "grDevices" >> [7] "utils" "datasets" "base" >> >> other attached packages: >> rat2302cdf affyQCReport simpleaffy genefilter survival >> affy >> "1.14.0" "1.12.0" "2.8.0" "1.12.0" "2.31" >> "1.12.1" >> affyio Biobase >> "1.2.0" "1.12.2" >> >> Thanks a lot! >> Juan >> >> _______________________________________________ >> 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 > > -- > Martin Morgan > Bioconductor / Computational Biology > http://bioconductor.org > > _______________________________________________ > 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 > -- Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center http://bioconductor.org
ADD COMMENTlink written 12.5 years ago by Seth Falcon7.4k
Answer: problem with function rma
0
gravatar for Seth Falcon
12.5 years ago by
Seth Falcon7.4k
Seth Falcon7.4k wrote:
Seth Falcon <sfalcon at="" fhcrc.org=""> writes: > Martin Morgan <mtmorgan at="" fhcrc.org=""> writes: >> R 2.5.0 is out, and so are the 1.14.x series of affy and Biobase. One >> thing that will change when you update is that affy will produce an >> eSet-based AffyBatch, which is slightly different: >> >> 1) update any old instances with rat <- updateObject(RatData) >> >> 2) use read.AnnotatedDataFrame rather than read.phenoData. >> > > Just to clarify: if you want to upgrade to the latest BioC packages, > you need to also upgrade to the latest release of R. > > Based on your sessionInfo, it looks like you have a mix since you have > affy 1.14.0 (part of BioC 2.0 release) and your other packages are > part of the 1.9 release and appropriate for your version of R. My comment here is bogus; I completely misread the sessionInfo output. Sorry about that. > Did you install via some mechanism other than biocLite? In any case, > mixing versions like this is not supported. I would recommend > upgrading your R and reinstalling BioC using biocLite. I still recommend upgrading :-) >>> other attached packages: >>> rat2302cdf affyQCReport simpleaffy genefilter survival >>> affy >>> "1.14.0" "1.12.0" "2.8.0" "1.12.0" "2.31" >>> "1.12.1" >>> affyio Biobase >>> "1.2.0" "1.12.2" Anyone have a suggestion of how R could format the sessionInfo output so that when it is cut/pasted into an email message it is readable? + seth -- Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center http://bioconductor.org
ADD COMMENTlink written 12.5 years ago by Seth Falcon7.4k
Seth Falcon wrote: > Seth Falcon <sfalcon at="" fhcrc.org=""> writes: > > >>Martin Morgan <mtmorgan at="" fhcrc.org=""> writes: >> >>>R 2.5.0 is out, and so are the 1.14.x series of affy and Biobase. One >>>thing that will change when you update is that affy will produce an >>>eSet-based AffyBatch, which is slightly different: >>> >>>1) update any old instances with rat <- updateObject(RatData) >>> >>>2) use read.AnnotatedDataFrame rather than read.phenoData. >>> >> >>Just to clarify: if you want to upgrade to the latest BioC packages, >>you need to also upgrade to the latest release of R. >> >>Based on your sessionInfo, it looks like you have a mix since you have >>affy 1.14.0 (part of BioC 2.0 release) and your other packages are >>part of the 1.9 release and appropriate for your version of R. > > > My comment here is bogus; I completely misread the sessionInfo > output. Sorry about that. > > >>Did you install via some mechanism other than biocLite? In any case, >>mixing versions like this is not supported. I would recommend >>upgrading your R and reinstalling BioC using biocLite. > > > I still recommend upgrading :-) > > >>>>other attached packages: >>>> rat2302cdf affyQCReport simpleaffy genefilter survival >>>>affy >>>> "1.14.0" "1.12.0" "2.8.0" "1.12.0" "2.31" >>>>"1.12.1" >>>> affyio Biobase >>>> "1.2.0" "1.12.2" > > > Anyone have a suggestion of how R could format the sessionInfo output > so that when it is cut/pasted into an email message it is readable? options(width=50) sessionInfo() Works for Thunderbird at least. Best, Jim > > + seth > -- James W. MacDonald University of Michigan Affymetrix and cDNA Microarray Core 1500 E Medical Center Drive Ann Arbor MI 48109 734-647-5623 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.
ADD REPLYlink written 12.5 years ago by James W. MacDonald51k
Answer: problem with function rma
0
gravatar for Steven McKinney
12.5 years ago by
Steven McKinney310 wrote:
>> Anyone have a suggestion of how R could format the sessionInfo output >> so that when it is cut/pasted into an email message it is readable? >> >> + seth search() produces an email-proof list > search() [1] ".GlobalEnv" "package:Matrix" "package:lattice" "tools:RGUI" "package:stats" "package:graphics" [7] "package:grDevices" "package:utils" "package:datasets" "package:methods" "Autoloads" "package:base" how about > sessionInfo() [1] "rat2302cdf:1.14.0" "affyQCReport:1.12.0" etc. Steve McKinney -----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch on behalf of Seth Falcon Sent: Wed 5/30/2007 9:33 AM To: bioconductor at stat.math.ethz.ch Subject: Re: [BioC] problem with function rma Seth Falcon <sfalcon at="" fhcrc.org=""> writes: > Martin Morgan <mtmorgan at="" fhcrc.org=""> writes: >> R 2.5.0 is out, and so are the 1.14.x series of affy and Biobase. One >> thing that will change when you update is that affy will produce an >> eSet-based AffyBatch, which is slightly different: >> >> 1) update any old instances with rat <- updateObject(RatData) >> >> 2) use read.AnnotatedDataFrame rather than read.phenoData. >> > > Just to clarify: if you want to upgrade to the latest BioC packages, > you need to also upgrade to the latest release of R. > > Based on your sessionInfo, it looks like you have a mix since you have > affy 1.14.0 (part of BioC 2.0 release) and your other packages are > part of the 1.9 release and appropriate for your version of R. My comment here is bogus; I completely misread the sessionInfo output. Sorry about that. > Did you install via some mechanism other than biocLite? In any case, > mixing versions like this is not supported. I would recommend > upgrading your R and reinstalling BioC using biocLite. I still recommend upgrading :-) >>> other attached packages: >>> rat2302cdf affyQCReport simpleaffy genefilter survival >>> affy >>> "1.14.0" "1.12.0" "2.8.0" "1.12.0" "2.31" >>> "1.12.1" >>> affyio Biobase >>> "1.2.0" "1.12.2" Anyone have a suggestion of how R could format the sessionInfo output so that when it is cut/pasted into an email message it is readable? + seth -- Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center http://bioconductor.org _______________________________________________ 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 COMMENTlink written 12.5 years ago by Steven McKinney310
Answer: problem with function rma
0
gravatar for Seth Falcon
12.5 years ago by
Seth Falcon7.4k
Seth Falcon7.4k wrote:
"Steven McKinney" <smckinney at="" bccrc.ca=""> writes: >>> Anyone have a suggestion of how R could format the sessionInfo output >>> so that when it is cut/pasted into an email message it is readable? >>> >>> + seth > > search() produces an email-proof list > >> search() > [1] ".GlobalEnv" "package:Matrix" "package:lattice" "tools:RGUI" "package:stats" "package:graphics" > [7] "package:grDevices" "package:utils" "package:datasets" "package:methods" "Autoloads" "package:base" > > how about > >> sessionInfo() > > [1] "rat2302cdf:1.14.0" "affyQCReport:1.12.0" Nice observation. I would find this much easier. Thanks for the suggestion. + seth -- Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center http://bioconductor.org
ADD COMMENTlink written 12.5 years ago by Seth Falcon7.4k
Answer: problem with function rma
0
gravatar for Seth Falcon
12.5 years ago by
Seth Falcon7.4k
Seth Falcon7.4k wrote:
"James W. MacDonald" <jmacdon at="" med.umich.edu=""> writes: > options(width=50) > sessionInfo() > > Works for Thunderbird at least. Yes, but then we would have to start telling people: Please send us your session info. Before you do, set options width=50... In an R session, sessionInfo() is readable, but it rarely crosses the cut/paste barrier unscathed. -- Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center http://bioconductor.org
ADD COMMENTlink written 12.5 years ago by Seth Falcon7.4k
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ADD REPLYlink written 12.5 years ago by Lev Soinov470
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