[Bioc-devel] affyQA/QC
Robert Gentleman wrote:
Hi, I am trying to put together a set of, what one might regard, as standard plots and summary statistics that should be collected on any set of Affymetrix microarrays (at least ones for gene expression). The first pass is attached, I would appreciate any comments on it, especially with regard to things that I have missed, or things I have suggested that don't seem to be quite correct, or could be improved. On an implementation note - I will be making use of existing software and intend to work with Craig Parman to put this into the existing affyQCReport package - users of that might want to let me know what functionality they are relying on, but this should be strict additions.
Hi Robert, For 5, I usually rely on a plot of the first two principal components rather than something like a heatmap. Although a PCA plot is less familiar to Biologists, it is certainly less expensive to make, and IMO, easier to interpret. Best, Jim
thanks Robert ------------------------------------------------------------------------
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