[BioC] NA/NaN/Inf in foreign function call in mas5calls function

[James W. MacDonald]

Hi Kartik,

Karthik Ramaswamy Padmanabhan wrote:
> Hello,
> 
> I am trying to process some CEL files using the affy package in Bioconductor. I am using the steps given in the Bioconductor manual given here - http://manuals.bioinformatics.ucr.edu/home/R_BioCondManual#biocon_affypack
> 
> Here is the list of commands I used:
> 
> mydata <- ReadAffy(cdfname = "hugene10stv1.r3cdf")
>> eset <- rma(mydata)
> Background correcting
> Normalizing
> Calculating Expression
>> eset_PMA <- mas5calls(mydata)
> Getting probe level data...
> Computing p-values
> Error in FUN(1:10[[1L]], ...) : 
>   NA/NaN/Inf in foreign function call (arg 2)
> 
> So, I am getting an error in the mas5calls function. Here is the sessionInfo():

And you should expect to. The HuGene chip is a PM-only chip, so trying 
to do MAS5 on it is not going to work.

Best,

Jim


> 
> R version 2.10.1 (2009-12-14) 
> x86_64-apple-darwin9.8.0 
> 
> locale:
> [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
> 
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base     
> 
> other attached packages:
> [1] hugene10stv1.r3cdf_2.5.0 affy_1.24.2             
> [3] Biobase_2.6.1           
> 
> loaded via a namespace (and not attached):
> [1] affyio_1.14.0        preprocessCore_1.8.0 tools_2.10.1 
> 
> And here is the traceback():
> 
> 7: .C("DetectionPValue", as.double(pms[, x]), as.double(mms[, x]), 
>        as.character(pns), as.integer(length(mms[, x])), as.double(tau), 
>        as.double(sat), dpval = double(length(unique.pns)), length(unique.pns), 
>        PACKAGE = "affy")
> 6: FUN(1:10[[1L]], ...)
> 5: lapply(X, FUN, ...)
> 4: sapply(1:length(pms[1, ]), function(x) {
>        .C("DetectionPValue", as.double(pms[, x]), as.double(mms[, 
>            x]), as.character(pns), as.integer(length(mms[, x])), 
>            as.double(tau), as.double(sat), dpval = double(length(unique.pns)), 
>            length(unique.pns), PACKAGE = "affy")$dpval
>    })
> 3: mas5calls.AffyBatch(object, ...)
> 2: mas5calls(mydata)
> 1: mas5calls(mydata)
> 
> Kindly let me know if I am missing something, or whether it is possible that there is something wrong with the data. I tried using the "Dilution" dataset, and it seems to work. Thanks in advance.
> 
> 
> Warm Regards
> 
> Karthik Ramaswamy Padmanabhan
> 
> M.S in Bioinformatics
> Indiana University, Bloomington
> 
> 
> 
> 
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> 
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