Automated Quality Analysis Pipeline For Affymetrix Gene St Arrays?

Question

[Adam Cornwell]

I've been using automated quality report tools such as affyAnalysisQC for looking at array dataset quality for some time now. However, most packages/systems for that purpose (in Bioconductor or otherwise) don't support the whole transcript-style Gene ST arrays. In the case of R packages, most of the packages used the Affy package to read in the array data, and Affy wasn't designed for & no longer supports the new style arrays. Does any pipeline for QC that supports these arrays exist? Affy's own ExpressionConsole is not very useful or much fun to work with. In the end it seems like I might just want to customize affyAnalysisQC to support these, but I won't have time to work on that for a while.

Edit: arrayQualityMetrics works. Are there any others? ArrayTools apparently supports GeneST 1.0, but it uses annotation bundled with it and I'm working with Gene ST 2.0

Thanks!

Answer 1

[Charles Warden]

I know for certain that Partek will work for this purpose, but it is commercial software (although you could get a temporary demo license)

I'm sure there must also be solution within Bioconductor, so hopefully someone can chime in with a direct answer. My guess is that downloading a library including an annotation file for the ST 2.0 array should probably enable most packages to work with that array design (especially if you know they work with 1.0 ST arrays or U133 arrays):

http://bioconductor.org/packages/2.13/data/annotation/html/pd.hugene.2.0.st.html