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

[Matthew McCormack]

Hi Wolfgang,

     I downloaded the most recent version of arrayQualityMetrics and 
everything is working fine now. Thanks for writing this very helpful 
package.

Matthew

On 12/6/2011 5:24 PM, Wolfgang Huber wrote:
> 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
>>
>>
>> The information in this e-mail is intended only for t...{{dropped:21}}