[Bioc-devel] pval in mas5calls()

[cstrato]

Dear Martin

Thank you for your immediate reply, it works great.
(Maybe this could be mentioned in the help file for ?mas5calls)

Best regards
Christian

Martin Morgan wrote:
> Christian:
>
> The values are there, just not accessible with se.exprs. Try
> 'assayData(obj)[["se.exprs"]]':
>
>   
>> example(mas5calls)
>>     
>
> ms5cll> data(affybatch.example)
>
> ms5cll> PACalls <- mas5calls(affybatch.example)
> Getting probe level data...
> Computing p-values
> Making P/M/A Calls
>   
>> dim(assayData(PACalls)[["se.exprs"]])
>>     
> [1] 150   3
>
> Martin
>
> cstrato <cstrato at aon.at> writes:
>
>   
>> Dear all,
>>
>> Could it be that function mas5calls() no longer returns the p-values, 
>> since se.exprs does no longer exist?
>>
>> I get:
>> pr.call <- mas5calls(pr)
>> call <-exprs(pr.call)
>> pval <-se.exprs(pr.call) ||
>> Error in function (classes, fdef, mtable)  :
>>         unable to find an inherited method for function "se.exprs", for 
>> signature "ExpressionSet"
>>
>> Interestingly, the source code in "mas5.R" still creates an 
>> ExpressionSet with "se.exprs=p".
>>
>> sessionInfo()
>> R version 2.5.0 (2007-04-23)
>> i386-apple-darwin8.9.1
>>
>> locale:
>> C
>>
>> attached base packages:
>> [1] "tools"     "stats"     "graphics"  "grDevices" "utils"     "datasets"
>> [7] "methods"   "base"    
>>
>> other attached packages:
>> hgu95av2cdf        affy      affyio     Biobase
>>    "1.16.0"    "1.14.0"     "1.4.0"    "1.14.0"
>>
>> Best regards
>> Christian
>>
>> _______________________________________________
>> Bioc-devel at stat.math.ethz.ch mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>     
>
>