Hello, We are looking at some HG-U133A arrays in which the RNA degredation plot shows a large increase from 5' to 3'. Is it neccessarily bad? Is there a condition on the slope that defines "bad"? Here are the slopes and pvs. slope 1.88 1.34 1.86 1.71 pvalue 1.94e-07 3.74e-05 1.14e-07 6.48e-07 Any advice, or pointers to references would be appreciated. Harry Hurd [[alternative HTML version deleted]]

I don't think there is a consensus on what is and isn't 'bad' when considering the slope of the degradation plots. There was a recent thread on this list where somebody noted that the U133A chips always have a positive slope, so you are probably OK. In my opinion, the slope is not nearly as critical as consistency of the slopes, especially if you are doing something like rma where you are considering all the chips as a batch. Since the expression values are only meaningful when compared to other expression values in that batch, consistent problems with degradation/second strand synthesis should all come out in the wash. One other recourse is to eliminate the first few probes on the 5' end and see if you get different/better results. This would probably require some code hacking (I don't think this functionality exists right now), and you would also have to decide how many probes to remove as well as come up with some way to detect improvements in the expression values. HTH, Jim James W. MacDonald Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623 >>> "Harry Hurd" <hhurd1@nc.rr.com> 01/08/04 05:45PM >>> Hello, We are looking at some HG-U133A arrays in which the RNA degredation plot shows a large increase from 5' to 3'. Is it neccessarily bad? Is there a condition on the slope that defines "bad"? Here are the slopes and pvs. slope 1.88 1.34 1.86 1.71 pvalue 1.94e-07 3.74e-05 1.14e-07 6.48e-07 Any advice, or pointers to references would be appreciated. Harry Hurd [[alternative HTML version deleted]] _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor