Dear List,
 
When I run my script in R v 2.6.0 to create an expression set from scratch, I got the following error. I have run the same program in R v 2.5.1 and I did not get any problem. Could you help me? here is my script
 
> library(moe430a)
> library(tools)
> library(Biobase)
> exprsFile <- "c:/affy/Cochlea.txt"
> exprs <- as.matrix(read.table(exprsFile, header = TRUE, sep = "\t",row.name=1, as.is = TRUE))
> pDataFile<-"c:/affy/functional.txt"
> pData<-read.table(pDataFile,row.names=1,header=TRUE,sep="\t")
> sapply(pData, class)
    cluster      ABRAge       Freq3       Freq6      Freq12      Freq24 
   "factor"   "numeric"   "integer"   "integer"   "integer"   "integer" 
     Freq32      Freq48    DPOAEAge    Mean.Low Mean.Middle   Mean.High 
  "integer"   "integer"   "numeric"   "numeric"   "numeric"   "numeric" 
> names(pData)
 [1] "cluster"     "ABRAge"      "Freq3"       "Freq6"       "Freq12"     
 [6] "Freq24"      "Freq32"      "Freq48"      "DPOAEAge"    "Mean.Low"   
[11] "Mean.Middle" "Mean.High"  
> phenoData
  rowNames: A, B, ..., AN (40 total)
  varLabels and varMetadata:
    cluster: cluster
    ABRAge: ABRAge
    ...: ...
    Mean.High: Mean.High
    (12 total)

> metadata <- data.frame(labelDescription = c("cluster", "ABRAge", "Freq3","Freq6","Freq12","Freq24","Freq32","Freq48","DPOAEAge",
+ "Mean.Low","Mean.Middle","Mean.High"))
>  row.names = c("cluster","ABRAge", "Freq3","Freq6","Freq12","Freq24","Freq32","Freq48","DPOAEAge",
+ "Mean.Low","Mean.Middle","Mean.High")
> phenoData <- new("AnnotatedDataFrame", data = pData, varMetadata = metadata)
> annotation <- "moe430a"
> all(rownames(pData) == colnames(exprs))
[1] TRUE

> exampleSet <- new("ExpressionSet", exprs = exprs, phenoData = phenoData,
+ annotation="moe430a")
Error in .nextMethod(e1, e2) : 
  comparison of these types is not implemented

 
Thanks. 
Yolande

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