[Bioc-devel] affyQA/QC

James W. MacDonald jmacdon at med.umich.edu
Sat Sep 23 15:28:53 CEST 2006

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.



>  thanks
>    Robert
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James W. MacDonald
University of Michigan
Affymetrix and cDNA Microarray Core
1500 E Medical Center Drive
Ann Arbor MI 48109

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