[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 and a couple of 3' end positions. The mean 
intensity on both ends dropped dramatically relative to others.

I have observed several other RNA digestion plots of hg-U133plus2 chips 
from a different lab. Their plots were almost linear with slope ranging 
from 3 to 6. Most often it is 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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