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

[Wolfgang Huber]

Dear Matthew

Thank you for the report. It is difficult to say what is going on 
without more details. In general, please always make sure you are using 
the latest versions of Bioconductor, and include the output of 
sessionInfo().

Beyond that, in order to diagnose/fix your problem, we would need an R 
script that reproduces the error, and the necessary CEL files (maybe one 
or two already suffice?) or the AffyBatch object.

Best wishes
	Wolfgang


On 12/6/11 10:59 PM, Matthew McCormack wrote:
> 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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