Dear All, I am using bioconductor 2.1 (R2.6) to do the affy quality assessment ratioes on a set of 40 hgu133plus2 arrays. I have found that several of the parameters go outside the ranges mentioned in the article by Bolstad et al i"Preprocessing high Density Oligonucleotide arrays" in the book "Bioiioformatics and computational biology solutions using R and Bioconductor". 1. The average background values are supposed to be comparable to one another. The mean for the f0 slides is 65.6. the stdeve is 22.2. Only 2 slides are outside 2 stdevs of the mean. one at 120 and the other at 134. Should these slides be rejected on this basis? What is a good criterion for an avbg to be different? 2. The scale factors are supposed to be withjin 3 fold of one another. I have scale factors ranging from 0.386 to 3 with a median of about 1. Shoudl I throwoout as many arrays as I need form the ends until the highest remaining scale factor is within a factor of 3 of the lowest remaining sclae factor. I would loose about 6/40 arrays like this. Is this two stringent? I owuld appreciate any sugegstions. 3. My minimum % present is 34.5 by maximum 49.5 and my median 45.0. Am I correct that I need not through any arrays out on this basis. 4. All but a few of my actin3'5' and gapdh3'/5' ratioes are gretaer than 2. Does this pause a serious problem? The slopes are about the same and are alll within 2 standard deviations of the mean with the exception of one point which is in 2.5 standard deviations of the mean. Any guidance in this matter would be greatly appreciated. Thanks and best wishes, Rich ------------------------------------------------------------ Richard A. Friedman, PhD Biomedical Informatics Shared Resource Lecturer Department of Biomedical Informatics Educational Coordinator Center for Computational Biology and Bioinformatics National Center for Multiscale Analysis of Genomic Networks Box 95, Room 130BB or P&S 1-420C Columbia University Medical Center 630 W. 168th St. New York, NY 10032 (212)305-6901 (5-6901) (voice) friedman at cancercenter.columbia.edu http://cancercenter.columbia.edu/~friedman/ "The last 250 pages of the last Harry Potter book took place in one day because alot happened in that day. All of Ulysses takes place in one day and nothing happened in that day." -Rose Friedman, age 11