[BioC] creating expression set

[Martin Morgan]

Hi Yolande --

Thanks very much for that.

> R version 2.6.0 (2007-10-03)
> 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] tools     stats     graphics  grDevices utils     datasets  methods 
> [8] base    
>
> other attached packages:
> [1] Biobase_1.14.1

The Biobase you are using is version 1.14.1, but should be 1.16.1 to
work with R 2.6.0. There are instructions for updating packages at

http://www.bioconductor.org/docs/install-howto.html

under 'Update packages'. Be sure to do this in a new R session, and
please report back to the list, hopefully with success.

Martin

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

> Here it is.
>
>> traceback()
> 33: eval(expr, envir, enclos)
> 32: eval(call, callEnv)
> 31: callNextMethod(e1, e2)
> 30: classVersion(object)[names(vers)] == vers
> 29: classVersion(object)[names(vers)] == vers
> 28: isCurrent(object, class(object))
> 27: isCurrent(object, class(object))
> 26: isCurrent(object)
> 25: isCurrent(object)
> 24: isValidVersion(object, "eSet")
> 23: validMsg(NULL, isValidVersion(object, "eSet"))
> 22: validityMethod(as(object, superClass))
> 21: identical(x, TRUE)
> 20: anyStrings(validityMethod(as(object, superClass)))
> 19: validObject(.Object)
> 18: .nextMethod(.Object, ...)
> 17: eval(expr, envir, enclos)
> 16: eval(call, callEnv)
> 15: callNextMethod(.Object, ...)
> 14: .local(.Object, ...)
> 13: .nextMethod(.Object, assayData = assayData, phenoData = phenoData,
>         featureData = featureData, experimentData = experimentData,
>         annotation = annotation)
> 12: eval(expr, envir, enclos)
> 11: eval(call, callEnv)
> 10: callNextMethod(.Object, assayData = assayData, phenoData = phenoData,
>         featureData = featureData, experimentData = experimentData,
>         annotation = annotation)
> 9: .local(.Object, ...)
> 8: .nextMethod(.Object, phenoData = phenoData, featureData = featureData,
>        experimentData = experimentData, annotation = annotation,
>        exprs = exprs, ...)
> 7: eval(expr, envir, enclos)
> 6: eval(call, callEnv)
> 5: callNextMethod(.Object, phenoData = phenoData, featureData = featureData,
>        experimentData = experimentData, annotation = annotation,
>        exprs = exprs, ...)
> 4: .local(.Object, ...)
> 3: initialize(value, ...)
> 2: initialize(value, ...)
> 1: new("ExpressionSet", exprs = exprs, phenoData = phenoData, annotation =
> "moe430a")
>> sessionInfo()
> R version 2.6.0 (2007-10-03)
> 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] tools     stats     graphics  grDevices utils     datasets  methods 
> [8] base    
>
> other attached packages:
> [1] Biobase_1.14.1
>
> Thanks for your help.
>
> Yolande 
>
>
> ------------------------------------------------------------------------------
>
> From: Martin Morgan [mailto:mtmorgan at fhcrc.org]
> Sent: Tue 10/30/2007 11:13 AM
> To: Yolande Tra
> Cc: bioconductor at stat.math.ethz.ch
> Subject: Re: [BioC] creating expression set
>
>
> 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]]
>>
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