Dear list members, I applied the digestion plot to two different Affy chips (library affy v. 1.1.5, hgu133a_1.2.6, hgu95a_1.1.0, R 1.6.1). While for the U95Av2 the plots look like expected, I get a slope close to 1 for all chips on the U133A (see attached ppt slide, where identical biological samples were hybridised to both chips). I have observed similar things with some other chips (mouse or rat, can't remember right now but I can look it up if of interest). Is there a bug in the function AffyRNAdeg() or is this due to the new chip design? Thanks a lot -oli- Script used: deg <- AffyRNAdeg(data) summaryAffyRNAdeg(deg) plotAffyRNAdeg(deg) -- Oliver Hartmann, Institute of Medical Biometry and Epidemiology Philipps-University Marburg, Bunsenstr. 3, D-35037 Marburg phone +49(0)6421 28 66514, fax +49(0)6421 28 68921 -------------- next part -------------- A non-text attachment was scrubbed... Name: RNA digestion plot.zip Type: application/x-zip-compressed Size: 128609 bytes Desc: not available Url : https://www.stat.math.ethz.ch/pipermail/bioconductor/attachments /20030718/97b5e03b/RNAdigestionplot-0001.bin