I've gotten arrayQualityMetrics to work with an ExpressionSet, i.e.
post-processed data, but can't get it to work with pre-processed data
because I cannot make an affyBatch from the new Affy Rat Gene ST arrays.
Affy puts out a .qcc file but not a qcdef file for these arrays. I would
like to be able to look at pre-processed QA. Also, I miss some of the
features of affyQAReport such as Nuse plots, which have been very helpful to
me in identifying problem arrays.

Any suggestions?

Mark

Mark W. Kimpel MD  ** Neuroinformatics ** Dept. of Psychiatry
Indiana University School of Medicine

15032 Hunter Court, Westfield, IN  46074

(317) 490-5129 Work, & Mobile & VoiceMail
(317) 399-1219  Home
Skype:  mkimpel

"The real problem is not whether machines think but whether men do." -- B.
F. Skinner
******************************************************************


On Tue, Oct 14, 2008 at 12:07 PM, Robert Gentleman <rgentlem@fhcrc.org>wrote:

> My efforts now are in support of Audrey Kauffmann's arrayQualityMetrics
> package, which provide much more comprehensive support for QA on
> microarrays. Have you tried it?
>
> best wishes
>  Robert
>
>
> Mark Kimpel wrote:
>
>> I've become quite fond of affyQAReport and have numerous examples of cases
>> where I have used it to help identify problem arrays that my core
>> facility,
>> which uses only Affymetrix tools, have said are fine. I am now using the
>> Affy Rat Gene 1.0 ST array and apparently cannot convert it into an
>> affyBatch (required as input to affyQAReport) using the packages I have
>> been
>> steered to for analysis (oligo and pdInfoBuilder) . Is there another
>> package
>> or approach one can use to do QA on these newer chips? I did try hacking
>> affyQAReport, but ran into my own limitations when I got to the function
>> qc,
>> which sets a cdf environment variable.
>>
>> Mark
>> ------------------------------------------------------------
>> Mark W. Kimpel MD  ** Neuroinformatics ** Dept. of Psychiatry
>> Indiana University School of Medicine
>>
>> 15032 Hunter Court, Westfield, IN  46074
>>
>> (317) 490-5129 Work, & Mobile & VoiceMail
>> (317) 399-1219  Home
>> Skype:  mkimpel
>>
>> "The real problem is not whether machines think but whether men do." -- B.
>> F. Skinner
>> ******************************************************************
>>
>>        [[alternative HTML version deleted]]
>>
>> _______________________________________________
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>> https://stat.ethz.ch/mailman/listinfo/bioconductor
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>>
>>
> --
> Robert Gentleman, PhD
> Program in Computational Biology
> Division of Public Health Sciences
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N, M2-B876
> PO Box 19024
> Seattle, Washington 98109-1024
> 206-667-7700
> rgentlem@fhcrc.org
>

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