Hi Jim, just a follow-up to your post, when you referred to outliers on the density plot in discussing AffyRNAdeg slopes, is this a function within the AffyRNAdeg program? Best wishes, Mark "Anyway, in my experience, large differences in slope are less critical than big differences between the density plots. I find that outliers on the density plot nearly always require a redo of the chip, whereas chips with very different slopes in the RNA degradation plot may be usable." Marquis P. Vawter, Ph.D. Director, Functional Genomics Laboratory Department of Psychiatry & HB Medical Science - D433, Zot Code 1675 University of California, College of Medicine Irvine CA 92697-1675 Email mvawter@uci.edu <mailto:mvawter@uci.edu> Phone 949-824-9014 Fax 949-824-7012 Lab: Gillespie Neuroscience Bldg., Room 3226 Zot code 4260B. Lab: 949-824-9170

Vawter, Marquis wrote: > Hi Jim, just a follow-up to your post, when you referred to outliers on the > density plot in discussing AffyRNAdeg slopes, is this a function within the > AffyRNAdeg program? Best wishes, Mark No, it's just an eyeballometric measurement on my part. However, it appears that you might be confusing what I said. My point was that the results from the density plot (different looking curves) are usually much more indicative of how things are going to work out than the AffyRNAdeg plots (non-parallel lines). When I analyze Affy data, I always do the density and AffyRNAdeg plots as QC. If I have a chip or chips that look different (on the density plot), I will use the residual plots in the affyPLM package to see how well the medianpolish algorithm is fitting the data, and the 'outliers' usually have huge residuals. Another thing I like to do to QC the data is to do a principal components analysis of the expression values (e.g., after fitting RMA or GCRMA or whatever) and plot the first two principal components. If I don't get reasonable grouping of my samples on this plot it usually indicates that the replicates are not very similar, which almost never bodes well for the downstream analyses. Jim > "Anyway, in my experience, large differences in slope are less critical than > big differences between the density plots. I find that outliers on the > density plot nearly always require a redo of the chip, whereas chips with > very different slopes in the RNA degradation plot may be usable." > > > Marquis P. Vawter, Ph.D. > Director, Functional Genomics Laboratory > Department of Psychiatry & HB > Medical Science - D433, Zot Code 1675 > University of California, College of Medicine > Irvine CA 92697-1675 > > Email mvawter@uci.edu <mailto:mvawter@uci.edu> > Phone 949-824-9014 > Fax 949-824-7012 > > Lab: Gillespie Neuroscience Bldg., Room 3226 > Zot code 4260B. > Lab: 949-824-9170 > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor -- James W. MacDonald Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109