[BioC] arrayQualityMetrics subscript out of bounds error and Harshlight error

[Matthew McCormack]

I get the following error when I run arrayQualityMetircs on an affybatch 
file that has 13 Affymetrix CEL files:
Error in .local(object, ...) : subscript out of bounds

The full command is:
  arrayQualityMetrics(expressionset = abatch, outdir = 
"AQM_GT_Jos5236-5248_Dec_11", force = TRUE, do.logtransform = TRUE)

I also get the following error when running Harshlight on the same affy 
batch file:
Error in indices2xy(i, nr = object at nrow) :
   Indices must start at 0 or 1 (please refer to the help file) !

    I thought I would add the Harshlight error, because I'll bet the two 
are related.  I did not generate the .CEL files. I received them and put 
them into an affy batch file with the command
abatch <- ReadAffy()

    Any ideas as to what the problem is ?

Matthew


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