[BioC] Problem with affyQCReport

James W. MacDonald jmacdon at med.umich.edu
Fri Oct 23 17:25:11 CEST 2009

Hi Chris,

Man, Chris T. wrote:
> Hi all,
> I was trying to do affyQCReport on a set of affy human U133a chips, but I got the following error. Can anyone help please?
> Thanks.
> Chris
> Error in setQCEnvironment(cdfn) : 
>   Could not find array definition file ' hthgu133acdf.qcdef '. Simpleaffy does not know the QC parameters for this array type.
> See the package vignette for details about how to specify QC parameters manually.

You aren't using hgu133a chips. You are using hthgu133a chips, which 
aren't the same.

However the QC parameters for the hgu133a chips will probably be the 
same, so you should follow the hint above, which is to look at the 
package vignette for how you specify the QC parameters manually and then 
do so, using the parameters for the hgu133a chip (which are already 



> Error in plot(qc(object)) : 
>   error in evaluating the argument 'x' in selecting a method for function 'plot'
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James W. MacDonald, M.S.
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618

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