Hi Susan: > Does anyone have experience using limma with 2-color microarray data > obtained from the Applied Precision SoftWorx Tracker? I can read the > .txt files with read.maimages but I don't know how to create a Layout > for normalizeWithinArrays. It seems that I should be able to map the > Set/Set Row/Set Column values to Block/Row/Columns but I am not sure > about this. Any help would be much appreciated. So, Nirav purchased some cheap array scanner software for you to use? ;^) Just kidding... You should be able to create a layout for this object by creating a list with the following elements (note grid and block are interchangeable): ngrid.r <- # grid rows ngrid.c <- # grid columns nspot.r <- # rows within each grid nspot.c <- # columns within each grid ndups <- # duplicate spots spacing <- # spots between duplicate spots npins <- # print pins in the print head that printed the array start <- the starting point for printing each grid, i.e. "topleft" or "topright" Then, set rg$printer <- yourlist where yourlist is the list you created using the above map and rg is your RGList object. Good Luck!! Dave H -- David A. Henderson, Ph.D. Insightful Corporation 1700 Westlake Avenue North, Suite 500 Seattle, WA 98109-3044 Tel: 206-802-2307 Fax: 206-283-8691 DNADave at Insightful.Com http://www.insightful.com