Hi, This is a warning message for Bioconductor users who use NetAffx for their annotation rather than ?affyannot?. Affymetrix appears to have the order of its probes within the .csv files available on NetAffx (eg. HG-U133_Plus_2_annot121004) so that they are not the same as those appearing on in the RMA output, resulting in the errors in the assignation of intensity data to the correct annotations. For instance the order of probes seen after reading my HG-U133 Plus 2.0 .CEL files into LIMMA using RMA was: Probe ID Intensity1 Intensity 2 177_at 4.490467 4.501346 1773_at 6.147345 6.863805 However, the order of probes in the HU-U133_Plus_2_annot121004 file downloaded from NetAffx was: Probe ID Gene Title 1773_at farnesyltransferase, CAAX box, beta 177_at phospholipase D1, phophatidylcholine-specific which when copied and pasted into an excel spreadsheet of my normalized intensities resulted in the wrong annotations being assigned to the probes: Probe ID Intensity1 Intensity 2 Gene Title 177_at 4.490467 4.501346 farnesyltransferase, CAAX box, beta 1773_at 6.147345 6.863805 phospholipase D1, phophatidylcholine-specific In total 1129 probes were "out of order" between the two lists, and perhaps NetAffx users should consider using a "match" command on the Probe IDs of both lists to check that there are no errors being carried over to further analyses. Regards, Chehani Marie Chehani Alles Cancer Research Program Garvan Institute of Medical Research 384 Victoria Street, Darlinghurst 2010 Web: http://www.garvan.org.au Tel: (612) 9295 8354