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

[daphne mouzaki (RI)]

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