I have experiment with lots of arrays which are from a few different printings. In one of the printings, one plate was printed out of order. In another, the layout is slightly different from the rest (and is missing a few spots the others have). Consequently, I have three different gal files. I would like to analyze all the arrays together (to do some between slide normalization) and so would like to read them into the same marray object. It isn't clear to me how to do this. thanks, Scott Rifkin

Hi Scott, Every marrayraw object will only stores array from one print-run because we also specify the array layout information. I normalized within each print-run seprately and than combined the log-ratios. This will work nicely for most arrays. However, if you have duplicates spots for all probes, you will need to use functions in Limma to combined the print-runs. Cheers Jean ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Jean Yee Hwa Yang jean@biostat.ucsf.edu Lung Biology Center, Tel: (415) 476-3368 University of California, Fax: (415) 476-6014 500 Parnassus Avenue, MU 420-W, San Francisco, CA 94143-0560 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ On Fri, 2 Apr 2004, Scott Rifkin wrote: > I have experiment with lots of arrays which are from a few different > printings. In one of the printings, one plate was printed out of order. > In another, the layout is slightly different from the rest (and is missing > a few spots the others have). Consequently, I have three different gal > files. I would like to analyze all the arrays together (to do some > between slide normalization) and so would like to read them into the same > marray object. It isn't clear to me how to do this. > > thanks, > Scott Rifkin > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor >