For normalization the batches of slides do not matter if you use the usual 2-color normalization methods, which normalize each slide separately. If you want to do multi-array normalization, you need to read all the arrays into a single batch. However, for analysis, you likely want to use some type of ANOVA. For this, it is more convenient to read in all of the arrays in a single batch. At 09:18 AM 1/23/2004, Richard Friedman wrote: >Dear Bioconductor Users, > > I have a time course experiment using a dye swap There are 18 > slides in all, and a tiff file >for each slide.The slides may be described as > >condition1cy3-condition2cy5 time1 3 slides 6 tiff files >condition1cy5-condition2cy3 time1 3 slides 6 tiff files >condition1cy3-condition2cy5 time2 3 slides 6 tiff files >condition1cy5-condition2cy3 time2 3 slides 6 tiff files >condition1cy3-condition2cy5 time3 3 slides 6 tiff files >condition1cy5-condition2cy3 time3 3 slides 6 tiff files > >My question: In marrayinput, when I read in the files, preparatory to >normalization, >I have to use a file analogous to SwirlSample.txt in the example. In that >file, do >I read in: > >1. All 18 slides. >or >2. Just the 6 slides from the first time point, so that the slides from >the other 2 time points >should be read in and normalized in separate runs. > >Thanks and best wishes, >Rich >----------------------------------------------------------- >Richard A. Friedman, PhD >Associate Research Scientist >Herbert Irving Comprehensive Cancer Center >Oncoinformatics Core >Lecturer >Department of Biomedical Informatics >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@cancercenter.columbia.edu >http://cancercenter.columbia.edu/~friedman/ > >"Spring, Summer, and Winter. >Then Fall came along, >and that's the end of our song, >and the pigeons never hibernate at all". >-Rose Friedman, age 7 >(These are the correct lyrics and supersede >the version previously at the end of my sig) > >_______________________________________________ >Bioconductor mailing list >Bioconductor@stat.math.ethz.ch >https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor Naomi S. Altman 814-865-3791 (voice) Associate Professor Bioinformatics Consulting Center Dept. of Statistics 814-863-7114 (fax) Penn State University 814-865-1348 (Statistics) University Park, PA 16802-2111