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

[cstrato]

Dear Karthik,

Please note that the Affymetrix MAS5 algorithm requires both PM and MM 
values, and the HuGene (and HuExon) arrays do not have MM values. For 
this reason the "affy" package cannot run mas5calls for HuGene arrays.

As a note, my package "xps" allows to do mas5 and mas5.call for HuGene 
and HuExon arrays.  However, I would not recommend to use mas5.call for 
HuGene but use dabg.call, which is the algorithm Affymetrix has 
developed for HuGene/HuExon arrays and which is also available in xps.

Best regards
Christian
_._._._._._._._._._._._._._._._._._
C.h.r.i.s.t.i.a.n   S.t.r.a.t.o.w.a
V.i.e.n.n.a           A.u.s.t.r.i.a
e.m.a.i.l:        cstrato at aon.at
_._._._._._._._._._._._._._._._._._


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():
>
> 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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