For Affy QA function author(s),

I have been using several packages for QA of large affy chip set (~100 chips). I found a couple of issues with the current probe level graphic functions, for example. 

#1. The hist function in affy package doesn't attach a chip id to the corresponding histogram plot, so we don't know which histogram belongs to which chip. The affyQCReport package has a histogram function to embed a legend with color coding to differentiate histograms, but it doesn't work well with 100 chips. I'd like to attach the chip index near the peak of the histogram to make each histogram easily identifiable.

#2. The same holds true for the plotAffyRNAdeg function, I'd like to attach the chip index to the 3' end of line, so we can easily see which chip is irregular.

#3. ma.plot function in the affy package is pretty slow with probe level data, it renders a lot of data points in the output. When we come to export 100 MA plots with 6 MA plots per page in a PDF file, the file gets really big and navigation between pages becomes difficult.   I used a local weighted data point reduction sampling method to keep the contour and density profile of the MA plot while significantly reduce the data points. (I used such a method to retain similiar visual perspective with 5% data points).

if we can put these kind of considerations in the future release, it would increase the usability and performance for QA of large chip set without customization (as I currently do). 


Regards,
Ping Ling
JNJ



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