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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