Hi Everybody, I have a problem with the probe name (not the probe set name, but the probe name, i.e. “probeSetName+Indice”, like 1431_at1) and the order of probe between an affybatch and between the probe package information. For example with the 133A chips and the probe set “1431_at”: With the “hgu133aprobe” package, the order, for the 1431_at is: > as.data.frame(hgu133aprobe[hgu133aprobe$Probe.Set.Name=="1431_at",c(2, 3,4,5) ]) x y Probe.Set.Name Probe.Interrogation.Position 143 534 549 1431_at 1013 144 653 237 1431_at 1067 145 160 593 1431_at 1073 146 324 61 1431_at 1079 147 447 599 1431_at 1115 148 327 395 1431_at 1133 149 183 335 1431_at 1169 150 652 615 1431_at 1175 151 314 225 1431_at 1187 152 437 57 1431_at 1277 153 151 575 1431_at 1361 154 113 39 1431_at 941 155 677 607 1431_at 947 156 120 695 1431_at 953 157 248 585 1431_at 959 158 157 93 1431_at 965 If I read an affyBatch without normalisation and background correction, and I look for the pm of “1431_at” for the first and second experiment: > pm(anAffyBatch,"1431_at")[,c(1,2)] 1 2 1431_at1 2692.0 2837.0 1431_at2 252.8 340.8 1431_at3 105.3 106.0 1431_at4 112.0 133.0 1431_at5 243.0 226.3 1431_at6 952.3 790.0 1431_at7 707.5 806.0 1431_at8 520.8 687.3 1431_at9 2297.5 2797.8 1431_at10 1109.8 1218.0 1431_at11 594.3 757.8 1431_at12 560.8 563.0 1431_at13 950.0 1131.5 1431_at14 899.5 768.0 1431_at15 347.0 377.8 1431_at16 1628.0 2209.5 And now, if I read in a text editor (like emacs) the CEL file corresponding for the first experiment, and I check for the signal at (x,y) = (534 549), corresponding to the “first” probe in the hgu133aprobe , I obtained the line: 534 549 952.3 169.3 16 113 39 2692.0 195.2 16 And the signal “952.3” is not the signal of the “first” probe 1431_at1 in the affybatch what is “2692.0”, but correspond to the 6th in the affybatch : 1431_at6. If I search for the signal “2692.0” (the first PM in the affyBatch) in the CEL file, I have the line : 113 39 2692.0 195.2 16 And the coordinates (113,39) correspond of the 12th “row” in the hgu133aprobe. If you look at the ProbeInterogationPostition, in the hgu133aprobe, you have a “gap” between the 11th and 12th and if you order the information according to the ProbeInterogationPostion, when you obtained: > order(hgu133aprobe[hgu133aprobe$Probe.Set.Name=="1431_at",5]) [1] 12 13 14 15 16 1 2 3 4 5 6 7 8 9 10 11 And now, this order corresponds to the order in the affybatch, for this particular probeSet. So I have some questions: 1/ It’s seems that the order in an affybatch is based on the Probe.Intergogation.Position ? Is it true? Will it be always like that? 2/ I have no idea about the order in the hgu133aprobe. How is-it calculated? 3/ Is it possible to have a “harmonisation” of the two orders? 4/ How is it possible to simple merge an affybatch (the pm) and an hgu133aprobe (actually, I ordered the hgu133aprobe according to the Probe.Interrogation.Position and cbind the two data.frame, but it’s work only if the order in an affybatch is really based on this). Thanks for your helps, Bests. Laurent Buffat Laurent Buffat MD, PhD CSO It-Omics Parc Eurasanté 885, avenue Eugčne Avinée 59120 Loos Tél : 33 (0)3 20 16 40 56 [[alternative HTML version deleted]]