Hi, what is the relationship between the (x,y) coordinates of the cels on the chip, and the integer index j for the row in AffyBatch@exprs? The vignettes say: (Textual description of makecdfenv): j = x*nrow + y + 1 (Textual description of affy, p.26): j = x*nrow y + 1 (sic!) What coordinate system do the names "x" and "y" refer to? When looking at comparisons of chips of different types with common probes (e.g. MGU74A, MGU74Av2), and using Probe.X and Probe.Y as given in the CHIPNAME_probe_tab files from the netaffx website, it appears that the right mapping should be j = Probe.Y * nrow + Probe.X + 1 (for the perfect match) jmm = Probe.Y * nrow + Probe.X + 2 (for the mismatch) Is this correct? Best regards Wolfgang