Can someone please explain to me how to interpret the RNA degradation analysis (plot and slope) in the Affy package. I see little correlation between the slope calculated with this tool and the 5'/3' signal intensity ratio of the housekeeping genes (such as GAPDH and Actin) on the Affy arrays. What slope is considered an indication of degradation? Can you also please explain to me what the p-value refers to. Thanks, Mette Peters

I usually look at this plot as an indication of the consistency of my samples. The slope(s) will be different depending on the chip you use. For instance, a really good HG-U95av2 chip will have a slope approaching zero (for instance, the affy latin square data set are all consistently near zero). On the other hand, a U133A or U133plus2 will have a rather steep slope. Therefore, the slope is not necessarily informative. So rather than use the slope as a quality control metric, I simply look to see that the chips all have relatively similar slopes, which to me indicates consistent sample quality. However, I find that this plot is much less likely to point out a possible problem with my data. The density plot in my experience is a much better indicator of problematic chips. The p-value refers to the test of the null hypothesis that the slope = 0. If you have a very small p-value it indicates evidence that the slope is not zero. 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 >>> "Mette A. Peters" <mpeters1@u.washington.edu> 08/16/04 05:36PM >>> Can someone please explain to me how to interpret the RNA degradation analysis (plot and slope) in the Affy package. I see little correlation between the slope calculated with this tool and the 5'/3' signal intensity ratio of the housekeeping genes (such as GAPDH and Actin) on the Affy arrays. What slope is considered an indication of degradation? Can you also please explain to me what the p-value refers to. Thanks, Mette Peters _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor