Hello, Is there a way in Agi4x44PreProcess to filter out (i.e. change to NA) individual flagged signals? For example, if I do the probe filtering step as in the manual: ddFILT = filter.probes(ddNORM, control = TRUE, wellaboveBG = TRUE, + isfound = TRUE, wellaboveNEG = TRUE, sat = TRUE, PopnOL = TRUE, + NonUnifOL = T, nas = TRUE, limWellAbove = 75, limISF = 75, + limNEG = 75, limSAT = 75, limPopnOL = 75, limNonUnifOL = 75, + limNAS = 100, makePLOT = F, annotation.package = "hgug4112a.db", + flag.counts = T, targets) A feature with 5% of signals non-uniform (IsFeatNonUnifOL = 1) will pass. Unless I misunderstand something, this means the 5% of signals that were flagged will be included in the processed data set with no way to distinguish them. This will affect only a tiny percentage of my data but I'd still like to remove those values. Thanks in advance, Leslie *-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-* Leslie M. Turner, Ph.D. Payseur Lab University of Wisconsin Laboratory of Genetics Genetics/Biotechnology Building 425-G Henry Mall rm 2455 Madison, WI 53706 Phone: 608-262-6856 Fax: 608-262-2976 email: lturner3@wisc.edu [[alternative HTML version deleted]]