[BioC] RNA deg plot

[Jianping Jin]

Dear BioConductor,

I looked at RNA degradation for a hg-U133plus2 chip, which a lab ran for a 
pilot experiment(please see the attachment). The RNA digestion plot 
appeared fine except the 5' end probe and a couple of 3' end probes. The 
mean intensity on both end positions dropped dramatically relative to 
others.

I have observed several other RNA digestion plots of hg-U133plus2 chips run 
by different labs. These plots are almost linear with slope ranging from 3 
to 6. Most often it was 5' end probes that underwent significant RNA 
degradation. Does anyone have reasonable interpretation for the "drop down" 
plot? Any comments are highly appreciated.

JP JIn

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