question in read.exprSet and read.phenoData
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@marcelo-luiz-de-laia-377
Last seen 10.2 years ago
Hi everyone. I am trying to create an object exprSet using the function read.exprSet and I am not obtaining success. I already tried in several ways. 1.) Firts > KarinaSusc<-read.table("Ka_Susc.txt",header=TRUE,sep="\t",as.is=TRUE) > testFile <- tempfile() > write.table(KarinaSusc, testFile, quote = FALSE, sep = "\t", row.names + =TRUE, col.names = TRUE) > eSet <- read.exprSet(testFile) > eSet Expression Set (exprSet) with 7150 genes 7 samples phenoData object with 1 variables and 7 cases varLabels sample: arbitrary numbering 2.) Second > KarinaSusc<-read.table("Ka_Susc.txt",header=TRUE,row.names=1,sep="\t", as.is= TRUE) Error in "row.names<-.data.frame"(`*tmp*`, value = row.names) : duplicate row.names are not allowed *** I have the genes duplicate in the file (my nylon filter membrane had genes duplicate) 3.) Third > eSet <- read.exprSet("Ka_Susc.txt") > eSet Expression Set (exprSet) with 7150 genes 7 samples phenoData object with 1 variables and 7 cases varLabels sample: arbitrary numbering > pData(eSet) sample Gene 1 * this note is a sample! this is my colunm with the genes names SC1 2 SC2 3 SC3 4 ST1 5 ST2 6 ST3 7 4.) Fourth > read.phenoData("Ka_Susc.txt") phenoData object with 7 variables and 7151 cases varLabels V1: read from file V2: read from file V3: read from file V4: read from file V5: read from file V6: read from file V7: read from file I have 7150 genes and the 6 variables. I exported the exprSet "lymphoma" for a file txt and I compared with the one that I had created above and I could verify that they are different. How can I proceed to create an exprSet starting from my file of data? I have another file with 3575 genes (the average of the duplicates) My datafile is like this: Gene_ID SC1 SC2 SC3 ST1 ST2 ST3 gene1 30.2 1.9 32.2 7.4 1.1 8.4 gene2 ... SC1 = Untreated Replicate 1 SC2 = Untreated Replicate 2 SC3 = Untreated Replicate 3 ST1 = Treated Replicate 1 ST2 = Treated Replicate 2 ST3 = Treated Replicate 3 Thnaks very much Marcelo Luiz de Laia, M.Sc. Dep. de Tecnologia, Lab. Bioqu?mica e de Biologia Molecular Universidade Estadual Paulista - UNESP Via de Acesso Prof. Paulo Donato Castelane, Km 05 14.884-900 - Jaboticabal, SP, Brazil PhoneFax: 16 3209-2675/2676/2677 R. 202/208/203 (trab.) Phone res: 16 3203 2328 - www.lbm.fcav.unesp.br - mlaia@yahoo.com ---
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Entering edit mode
@marcelo-luiz-de-laia-377
Last seen 10.2 years ago
Dear All, To day I solve my problem. Thanks a lot... Marcelo > -----Original Message----- > From: bioconductor-bounces@stat.math.ethz.ch > [mailto:bioconductor-bounces@stat.math.ethz.ch]On Behalf Of Marcelo Luiz > de Laia > Sent: domingo, 2 de novembro de 2003 13:45 > To: Bioconductor > Subject: [BioC] question in read.exprSet and read.phenoData > > > Hi everyone. > > I am trying to create an object exprSet using the function > read.exprSet and > I am not obtaining success. > I already tried in several ways. ---
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