[BioC] RNA deg plot

Jianping Jin jjin at unc.edu
Thu Apr 28 19:32:17 CEST 2005

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 

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.


-------------- next part --------------
A non-text attachment was scrubbed...
Name: deg.png
Type: image/png
Size: 4066 bytes
Desc: not available
Url : https://stat.ethz.ch/pipermail/bioconductor/attachments/20050428/7467e781/deg.png

More information about the Bioconductor mailing list