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

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.

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