Hi there, I am using the code below to read and Expression set object into R. If I run the code below to R 2.5.1 it works and the expression set object is created to proceed with my analysis but in R 2.7.1 which I have I recently downloaded I get the error below. wd<-"M://Anna//Normal_Anal//Plier" setwd(wd) getwd() library(affy) library(limma) exprsFile <- "plier.txt" phenoDataFile <- "samples_listAll.txt" eset <- readExpressionSet(exprsFile, phenoDataFile, header=TRUE, sep="\t") str(eset) Error in readExpressionSet(exprsFile, phenoDataFile, header = TRUE, sep = "\t") : Column names of expression matrix must be identical to the sample names of the phenodata table. You could use 'options(error=recover)' to compare thevalues of 'sampleNames(pd)' and 'colnames(ex)'. This is the samples_listAll.txt(phenoDataFile) that I am trying to read in. The difference I noticed between the two R versions is that R 2.5 gives it the correct dimension 36 X 3 but R 2.7 reads it with dimensions 36 X 2. FileName Cell Sample 1356_0264_Kaliszewska_1396.plier mF U 1357_0264_Kaliszewska_1397.plier mF DI 1358_0264_Kaliszewska_1398.plier mF LI 1359_0264_Kaliszewska_1399.plier DC U 1360_0264_Kaliszewska_1400.plier DC DI 1361_0264_Kaliszewska_1401.plier DC LI 1362_0264_Kaliszewska_1402.plier mF U 1363_0264_Kaliszewska_1403.plier mF DI 1364_0264_Kaliszewska_1404.plier mF LI 1365_0264_Kaliszewska_1405.plier DC U 1366_0264_Kaliszewska_1406.plier DC DI 1367_0264_Kaliszewska_1407.plier DC LI 1368_0264_Kaliszewska_1408.plier mF U 1369_0264_Kaliszewska_1409.plier mF DI 1370_0264_Kaliszewska_1410.plier mF LI 1371_0264_Kaliszewska_1411.plier DC U 1372_0264_Kaliszewska_1412.plier DC DI 1373_0264_Kaliszewska_1413.plier DC LI 1374_0264_Kaliszewska_1414.plier mF U 1375_0264_Kaliszewska_1415.plier mF DI 1376_0264_Kaliszewska_1416.plier mF LI 1377_0264_Kaliszewska_1417.plier DC U 1378_0264_Kaliszewska_1418.plier DC DI 1379_0264_Kaliszewska_1419.plier DC LI 1380_0264_Kaliszewska_1420.plier mF U 1381_0264_Kaliszewska_1421.plier mF DI 1382_0264_Kaliszewska_1422.plier mF LI 1383_0264_Kaliszewska_1423.plier DC U 1384_0264_Kaliszewska_1424.plier DC DI 1385_0264_Kaliszewska_1425.plier DC LI 1386_0264_Kaliszewska_1426.plier mF U 1387_0264_Kaliszewska_1427.plier mF DI 1388_0264_Kaliszewska_1428.plier mF LI 1389_0264_Kaliszewska_1329.plier DC U 1390_0264_Kaliszewska_1330.plier DC DI 1391_0264_Kaliszewska_1330.plier DC LI Thanks in advance, Daphne ------------------------------------------- Daphne Mouzaki Statistician The Roslin Institute Roslin Midlothian EH25 9PS UK

Hi Daphne have you tried what the error message asks you to do, i.e. set options(error=recover) then go into the evaluation frame that corresponds to being in the readExpressionSet function, and print out the values of sampleNames(pd) colnames(ex) ? -- Best wishes Wolfgang ------------------------------------------------------------------ Wolfgang Huber EBI/EMBL Cambridge UK http://www.ebi.ac.uk/huber 14/07/2008 12:08 daphne mouzaki (RI) scripsit > Hi there, > > I am using the code below to read and Expression set object into R. > If I run the code below to R 2.5.1 it works and the expression set > object > is created to proceed with my analysis but in R 2.7.1 > which I have I recently downloaded I get the error below. > > wd<-"M://Anna//Normal_Anal//Plier" > setwd(wd) > getwd() > library(affy) > library(limma) > exprsFile <- "plier.txt" > phenoDataFile <- "samples_listAll.txt" > eset <- readExpressionSet(exprsFile, phenoDataFile, header=TRUE, > sep="\t") > str(eset) > Error in readExpressionSet(exprsFile, phenoDataFile, header = TRUE, sep > = "\t") : > Column names of expression matrix must be identical to > the sample names of the phenodata table. > You could use 'options(error=recover)' to compare thevalues of > 'sampleNames(pd)' and 'colnames(ex)'. > > > This is the samples_listAll.txt(phenoDataFile) that I am trying to read > in. > The difference I noticed between the two R versions is that R 2.5 gives > it the > correct dimension 36 X 3 but R 2.7 reads it with dimensions 36 X 2. > > FileName Cell Sample > 1356_0264_Kaliszewska_1396.plier mF U > 1357_0264_Kaliszewska_1397.plier mF DI > 1358_0264_Kaliszewska_1398.plier mF LI > 1359_0264_Kaliszewska_1399.plier DC U > 1360_0264_Kaliszewska_1400.plier DC DI > 1361_0264_Kaliszewska_1401.plier DC LI > 1362_0264_Kaliszewska_1402.plier mF U > 1363_0264_Kaliszewska_1403.plier mF DI > 1364_0264_Kaliszewska_1404.plier mF LI > 1365_0264_Kaliszewska_1405.plier DC U > 1366_0264_Kaliszewska_1406.plier DC DI > 1367_0264_Kaliszewska_1407.plier DC LI > 1368_0264_Kaliszewska_1408.plier mF U > 1369_0264_Kaliszewska_1409.plier mF DI > 1370_0264_Kaliszewska_1410.plier mF LI > 1371_0264_Kaliszewska_1411.plier DC U > 1372_0264_Kaliszewska_1412.plier DC DI > 1373_0264_Kaliszewska_1413.plier DC LI > 1374_0264_Kaliszewska_1414.plier mF U > 1375_0264_Kaliszewska_1415.plier mF DI > 1376_0264_Kaliszewska_1416.plier mF LI > 1377_0264_Kaliszewska_1417.plier DC U > 1378_0264_Kaliszewska_1418.plier DC DI > 1379_0264_Kaliszewska_1419.plier DC LI > 1380_0264_Kaliszewska_1420.plier mF U > 1381_0264_Kaliszewska_1421.plier mF DI > 1382_0264_Kaliszewska_1422.plier mF LI > 1383_0264_Kaliszewska_1423.plier DC U > 1384_0264_Kaliszewska_1424.plier DC DI > 1385_0264_Kaliszewska_1425.plier DC LI > 1386_0264_Kaliszewska_1426.plier mF U > 1387_0264_Kaliszewska_1427.plier mF DI > 1388_0264_Kaliszewska_1428.plier mF LI > 1389_0264_Kaliszewska_1329.plier DC U > 1390_0264_Kaliszewska_1330.plier DC DI > 1391_0264_Kaliszewska_1330.plier DC LI > > > Thanks in advance, > > Daphne > > ------------------------------------------- > Daphne Mouzaki > Statistician > The Roslin Institute > Roslin > Midlothian EH25 9PS > UK > > _______________________________________________ > 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