[BioC] Exception thrown in ReadAffy() when reading Hu-133B files in a GEO Dataset

[Peterson, Leif]

When using the straightforward "ReadAffy()" syntax to read Affy arrays, I am experiencing an exception which is being thrown when the reader hits HU133B file in a particular GEO dataset.   Is there an optimal way to read Hu-133A arrays separately from HU-133B arrays (.CEL files) from an untarred GEO data set?   

Thus, far, I am attempting a workaround by generating a filename list during untarring, and then attempting to read CEL files separately, using: 

dirname="C:/Data/GEOBreastHu133Plus/GSE1456/"
setwd(dirname)
rawcelfilename<-"C:/Data/GEOBreastHu133Plus/GSE1456/GSE1456_RAW.TAR"     
untar(rawcelfilename)
filelist<-untar(rawcelfilename,list=TRUE)
for (file in filelist) {
  result <- try(ReadAffy(filenames=file));
  if(class(result) != "try-error"){
  # data<- data + ???    <-- NEED to build up data set here after successfully opening each HU133A (B) CEL file
  }  
} 

If an exception is thrown due to an HU133B array, I want to go to the next filename.  The trick is also how to build up a data set based on the successfully read CEL files -- and the above is not working.

Later on, once "data" are read, I can use:

pset <- fitPLM(data)
NUSE(pset,main="GSE1456")
eset<- rma(data)
write.exprs(eset,file="data.txt")
save(eset, file = paste("GSE1456",".RData"))


FYI, I have successfully used:

data<- ReadAffy()

for HU133Plus2.0 CEL files and have had no problem; however, the Hu133B in this particular GEO set (1456) results in a thrown exception since HU133A arrays are not readable in ReadAFfy by default.  

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