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 -------------- 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 /4f377db0/deg.png

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 -------------- 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