[BioC] creating expression set

[Martin Morgan]

Hi Yolande --

can you provide the output of traceback() after the error? This will
help localize where the error is occurring. Also, to eliminate problems
with version mismatch, can you provide the output of sessionInfo()?

Thank you,

Martin

"Yolande Tra" <yvtsma at rit.edu> writes:

> 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
>
> 	[[alternative HTML version deleted]]
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor