hi, i'm confused about one line in the bg.correct.mas function (file bg.Affy.chipwide.R, line 11). there it says: ally <- c(pm.index, mm.index) %/% nrow(object) + 1 to calculate the y-coordinates of the pmormm probes, i persume. now i.e. (640*640) %/% 640 +1 = 641 --> should'nt it rather be something like ally <- (c(pm.index, mm.index) -1) %/% nrow(object) + 1 ? also i'm not sure if x and y are swapped, but of course this is of no concern calculating the background. a second thing is, that the 'non pm or mm probes' are not used. can maybe someone give me a hint where to find out what they actually are (grid alignment checkerboards, text, center cross or something like this??) . the reason for the question is, that respecting the 'nonpmormm's i observed a lower mean background estimate. thnx, dennis --Max-Planck-Institute for Molecular Genetics Computational Molecular Biology Ihnestrasse 63-73 D-14195 Berlin -- Tel: ++49 (30) 8413-1178 Fax: ++49 (30) 8413-1152

> a second thing is, that the 'non pm or mm probes' are not used. can maybe > someone give me a hint where to find out what they actually are (grid > alignment checkerboards, text, center cross or something like this??) . the > reason for the question is, that respecting the 'nonpmormm's i observed a > lower mean background estimate. My reading of the "Statistical Algorithms Description Document", which is my source material for the , says that control cells are not used in the calculation of the background. Thanks, Ben

Having gotten rather weary of all the "My MAS numbers from 'affy' differ from those I have gotten from Affymetrix MAS 5.0" type questions I have made a rather brief attempt to quantify the differences. For those interested point your browsers to http://www.stat.berkeley.edu/~bolstad/MAS5diff/Mas5difference.html At least in my mind the differences (which I will admit exist) are not incredibly drastic. The next time someone brings up this issue I'd hope they'd at least make an attempt to quantify the differences as I have. It is much more helpful to say where and by how much your values differ. The source is all open, so if you see a reason why there might be a difference you are free to modify the code, see if it helps and let us know about it. Thanks, Ben