[BioC] Differences in readExpressionSet between R2.7.1 and R2.5.1 version

[Wolfgang Huber]

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
> 
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