Thank you so much. I will try this as soon as I can. On 2013-11-17 10:23 PM, "Martin Morgan" <mtmorgan@fhcrc.org> wrote: > On 11/17/2013 12:11 PM, Jobin K. Varughese wrote: > >> Hello again. I was informed that I should share this as a public Dropbox >> link rather than as an attachment. This link can be found here: >> https://dl.dropboxusercontent.com/u/6322354/ExpressionSet_error.zip >> > > Hi Jobin -- I installed and loaded the package then > > debug(loadReadCounts) > source("stats.R") > > and then stepped through the function until I got to > > res <- new("shrnaSet", assayData=adata, phenoData=pdata, > featureData=fdata) > > when I ran this I got the error > > Browse[2]> new("shrnaSet", assayData=adata, phenoData=pdata, > featureData=fdata) > Error in validObject(.Object) : > invalid class "shrnaSet" object: featureNames differ between assayData > and featureData > > so I looked at the rownames of the objects inside adata, and the rownames > of fdata, which are supposed to be the same > > Browse[2]> eapply(adata, function(x) head(rownames(x))) > $readCounts1 > [1] "X4501844.NM_001088.1.38903" "X4501844.NM_001088.1.38904" > [3] "X4501844.NM_001088.1.38905" "X4501844.NM_001088.1.38906" > [5] "X4501844.NM_001088.1.38907" "X4501844.NM_001088.1.54352" > > $readCounts2 > [1] "X4501844.NM_001088.1.38903" "X4501844.NM_001088.1.38904" > [3] "X4501844.NM_001088.1.38905" "X4501844.NM_001088.1.38906" > [5] "X4501844.NM_001088.1.38907" "X4501844.NM_001088.1.54352" > > Browse[2]> head(rownames(pData(fdata))) > [1] "4501844|NM_001088.1|38903" "4501844|NM_001088.1|38904" > [3] "4501844|NM_001088.1|38905" "4501844|NM_001088.1|38906" > [5] "4501844|NM_001088.1|38907" "4501844|NM_001088.1|54352" > > They're not the same, because earlier in the code the package author had > made the names of the assay data with 'make.names' > > x <- read.delim(file=paste(dataPath,condition2,sep="/"), header=TRUE) > condition2 <- as.matrix(x[,2:dim(x)[2]]) > rownames(condition2) <- make.names(x[,1],unique=TRUE) > > but the names of the feature data were not mangled > > fdat = read.delim(file=paste(dataPath,shRNAData,sep="/"), header=TRUE) > rownames(fdat) <- fdat[,1] > > I guess a work-around would be to mangle the names of the first column of > shRNALibrary.txt using make.names(). I think I would have written the code > above without mangling names as > > condition2 = as.matrix(read.delim(file.path(dataPath, condition2), > header=TRUE, row.names=1)) > > and (with similar changes elsewhere in this code) > > fdat = read.delim(file.path(dataPath,shRNAData), header=TRUE, > row.names=1) > > Martin > > >> Thank you. >> >> Jobin >> >> >> On Sat, Nov 16, 2013 at 1:25 PM, Jobin K. Varughese <jobinv@gmail.com>> >wrote: >> >> Hello. My name is Jobin K. Varughese MD PhD, and I work at the University >>> of Bergen, Norway. >>> >>> My issue is that I am having trouble with the ExpressionSet class. It >>> appears when running the following command (adapted from the shRNAseq< >>> http://rock.icr.ac.uk/software/shrnaseq.jsp>vignette): >>> >>> library(shRNAseq) >>>> dataPath <- ".." >>>> >>>> x <- loadReadCounts( >>>> >>> + screenData="phenoData.txt", >>> + shRNAData="shRNALibrary.txt", >>> + condition1="raw_tmz.txt", condition1Name="TMZ", >>> + condition2="raw_ctrl.txt", condition2Name="Control", >>> + dataPath=dataPath) >>> >>> Error in validObject(.Object) : >>> invalid class “shrnaSet” object: featureNames differ between >>> assayData and featureData >>> >>> I've made sure that the featureNames are indeed identical between the >>> various files. Next, I tried contacting the developer of shRNAseq and >>> even >>> sent him my raw data files. He attempted several strategies to solve the >>> issue: *"I've changed the names in the first columns to numbers 1:27500 >>> and made sure they match exactly between the files - didn't help. I've >>> checked line endings (Mac/Unix/Windows) - didn't help. I've removed the >>> final blank lines - didn't help. I've stripped quotes - didn't help."* >>> >>> Eventually he also was unable to get past the error message, but could >>> provide the following: *"The shRNAset object is basically an expression >>> set (Eset) and the methods are inherited from that (including the error >>> message)."* >>> >>> The error is reproducible with the sample files that I've attached >>> (compressed with 7zip). I have also attached the output from >>> sessionInfo() >>> and traceback(). >>> >>> Can anyone advise me as to what might be the problem? I would be very >>> grateful indeed. >>> >>> Sincerely, >>> Jobin K. Varughese >>> >>> >> [[alternative HTML version deleted]] >> >> >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: http://news.gmane.org/gmane. >> science.biology.informatics.conductor >> >> > > -- > Computational Biology / Fred Hutchinson Cancer Research Center > 1100 Fairview Ave. N. > PO Box 19024 Seattle, WA 98109 > > Location: Arnold Building M1 B861 > Phone: (206) 667-2793 > [[alternative HTML version deleted]]