I am a graduate student and new in the field of microarray data analysis. I am learning how to handle affymatrix's genechip arrays. In my data set there are 16 arrays. Image plot shows a dark horizontal area in the middle of the images. There are also two little bright areas in the images of all the arrays. The dark horizontal strip and the spots are in about the same position of the images (probe level data). What needs to be done to correct these(If at all)? Could anybody please mention some relevant references. Can I also background correct the probe level data independently (not within RMA)? I will appreciate your response. Thanks. Ariful Department of Statistical Science Southern methodist University Dallas, TX

Hi Ariful, Are these recent generation chips (hgu133plus2 or rat2302 or mouse4302)? With these chips there is usually a pronounced dark band across the middle of the image. I don't know if it is simply a moire pattern of some kind or actually because those probes are hybridizing less, but I almost always see this. As for the bright areas, are they directly in the middle of the chip, with possibly another bright area in the upper left corner? If so, these are different control probes, some of which should be nearly saturated. As long as the things you see are consistent from chip to chip, you are probably OK. Problems usually arise when you have e.g., a much brighter chip, or a big white blotch in the middle of a chip, etc. And yes, you can background correct separately. See ?bg.correct You might also try help.start() and peruse the help files for the affy package. This is a great place to start. 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 >>> "Islam, Ariful" <aislam at="" mail.smu.edu=""> 06/27/05 3:54 PM >>> I am a graduate student and new in the field of microarray data analysis. I am learning how to handle affymatrix's genechip arrays. In my data set there are 16 arrays. Image plot shows a dark horizontal area in the middle of the images. There are also two little bright areas in the images of all the arrays. The dark horizontal strip and the spots are in about the same position of the images (probe level data). What needs to be done to correct these(If at all)? Could anybody please mention some relevant references. Can I also background correct the probe level data independently (not within RMA)? I will appreciate your response. Thanks. Ariful Department of Statistical Science Southern methodist University Dallas, TX _______________________________________________ Bioconductor mailing list Bioconductor at stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.

Hi, I am new to microarray analysis and have been trying to use marray (in R 2.1.0) to read in data from GenePix (.gpr) files, but it hasn't worked... There are 6 .gpr files (e.g. samcellINF8a.gpr as below), the sample description .txt file and a .gal file in my directory (folder containing files is called Samsfish). I've been trying to copy the example in the vignette entittled "Quick Start Guide for marray". It worked fine up until the following line of code: > data <- read.GenePix(targets=SamsfishTargets) ...which gives me this error message: Error in file(con, "r") : unable to open connection In addition: Warning message: cannot open file './samcellINF8a.gpr' (or variations on a theme) Do you know what this means? What can I do about it? Many thanks, Amy ------------------------------------------- Amy Mikhail Research student University of Aberdeen Zoology Building Tillydrone Avenue Aberdeen AB24 2TZ Scotland Email: a.mikhail at abdn.ac.uk Phone: 00-44-1224-272880 (lab)