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)