[BioC] problem with function rma

[Juan Lin]

Hello Bioconductorers,

I am working with 12 affy rat2302 chips recently. It was OK when I tried to
read my cel files into R:

> RatData<-ReadAffy()
> list.celfiles()
 [1] "Rat 16hrs-1-2113.CEL"  "Rat 16hrs-2-2114.CEL"  "Rat 16hrs-3-2115.CEL"
 [4] "Rat 30hrs-1-2116.CEL"  "Rat 30hrs-2-2117.CEL"  "Rat 30hrs-3-2118.CEL"
 [7] "Rat 4hrs-1-2110.CEL"   "Rat 4hrs-2-2111.CEL"   "Rat 4hrs-3-2112.CEL"
[10] "Rat Normal-1-2107.CEL" "Rat Normal-2-2108.CEL" "Rat Normal-3-2109.CEL"

> phenoData(RatData) <- read.phenoData("phenoData.txt",header=T)
> show(pData(phenoData(RatData)))
                        ID time replicate
Rat Normal-1-2107.CEL 2107    0         1
Rat Normal-2-2108.CEL 2108    0         2
Rat Normal-3-2109.CEL 2109    0         3
Rat 4hrs-1-2110.CEL   2110    4         1
Rat 4hrs-2-2111.CEL   2111    4         2
Rat 4hrs-3-2112.CEL   2112    4         3
Rat 16hrs-1-2113.CEL  2113   16         1
Rat 16hrs-2-2114.CEL  2114   16         2
Rat 16hrs-3-2115.CEL  2115   16         3
Rat 30hrs-1-2116.CEL  2116   30         1
Rat 30hrs-2-2117.CEL  2117   30         2
Rat 30hrs-3-2118.CEL  2118   30         3

However, when I was going to do normalization, I got an error message as
following:

> esetRat <- rma(RatData)
Background correcting
Normalizing
Calculating Expression
Error in validObject(.Object) : invalid class "exprSet" object: sampleNames
different from names of phenoData rows

Can anyboday give me a clue on how to solve this problem?

BTW. my sessionInfor is as following:
> sessionInfo()
R version 2.4.0 (2006-10-03)
i386-pc-mingw32

locale:
LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
States.1252;LC_MONETARY=English_United
States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252

attached base packages:
[1] "splines"   "tools"     "methods"   "stats"     "graphics"  "grDevices"
[7] "utils"     "datasets"  "base"

other attached packages:
  rat2302cdf affyQCReport   simpleaffy   genefilter     survival
affy
    "1.14.0"     "1.12.0"      "2.8.0"     "1.12.0"       "2.31"
"1.12.1"
      affyio      Biobase
     "1.2.0"     "1.12.2"

Thanks a lot!
Juan