 When running the following code to update the phenoData for my eset, the 
resulting eset object works fine for downstream analysis.  However, when I 
try to subset the eset, I get the error noted just above the sessionInfo. 
Am I doing something wrong in the assignment, or should I not assign using 
the pData method?  This usage is still documented, so I assumed it was 
safe.  I know I'm getting some warning messages with the expressionSet in 
the example, but I get the same error when trying to subset a real dataset 
created using ReadAffy() and rma() without the corresponding warnings.

> data(sample.exprSet)
> expressionSet <- as(sample.exprSet,"ExpressionSet")
Warning messages:
1: The phenoData class is deprecated, use AnnotatedDataFrame (with 
ExpressionSet) instead 
2: The phenoData class is deprecated, use AnnotatedDataFrame (with 
ExpressionSet) instead 
> isCurrent(expressionSet)
            R       Biobase          eSet ExpressionSet 
         TRUE          TRUE          TRUE          TRUE 
> 
> expressionSet[1:10,c(2,4,10)]
ExpressionSet (storageMode: lockedEnvironment)
assayData: 10 features, 3 samples 
  element names: exprs, se.exprs 
phenoData
  rowNames: B, D, J
  varLabels and varMetadata:
    sex: Female/Male
    type: Case/Control
    score: Testing Score
featureData
  rowNames: AFFX-MurIL2_at, AFFX-MurIL10_at, ..., AFFX-BioDn-5_at (10 
total)
  varLabels and varMetadata: none
experimentData: use 'experimentData(object)'
Annotation [1] "hgu95av2"
> 
> p <- cbind (pData(expressionSet), sub("rol", "", 
pData(expressionSet)$type))
> names(p)[4] <- "type2"
> pData(expressionSet) <- p
> expressionSet[1:10,c(2,4,10)]
Error in `row.names<-.data.frame`(`*tmp*`, value = c("sex", "type", 
"score",  : 
        invalid 'row.names' length
> 
> sessionInfo()
R version 2.5.0 (2007-04-23) 
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] "tools"     "stats"     "graphics"  "grDevices" "utils"     "datasets" 

[7] "methods"   "base" 

other attached packages:
    affy   affyio  Biobase    limma 
"1.14.0"  "1.4.0" "1.14.0" "2.10.0" 
>

----------------------------------------
Stephen W. Edwards, Ph.D.
Systems Biologist, ADHIO, NHEERL, ORD, USEPA
U.S. Environmental Protection Agency (B305-01)
109 TW Alexander Drive
Research Triangle Park, NC  27711
Ph#: 919/541-0514       FAX#: 919/685-3221


	[[alternative HTML version deleted]]

