[BioC] can can affyQAReport (package affyQCReport) be adapted for use with Affy Gene ST arrays that are not incorporated into an affyBatch?

Robert Gentleman rgentlem at fhcrc.org
Tue Oct 14 18:07:31 CEST 2008

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

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]]
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor

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
rgentlem at fhcrc.org

More information about the Bioconductor mailing list