At 06:11 PM 18/08/2004, michael watson (IAH-C) wrote: > >Both read.maimages() and read.GenePix() are designed to read batches of >arrays all corresponding to > >the same GAL file. You cannot expect to read in data from different GAL >files at one time. > >I think this is a VERY important message for everyone who is a beginner >with bioconductor. > >All of the data read functions I have come across so far rely on the >files being in the same row-order. > >There is NO cross-referencing of Block/Col/Row or gene names across >files; bioconductor simply assumes that row 1 in file 1 corresponds to >row 1 in file 2, row2 in file 1 to row 2 in file 2 etc etc... > >In the vast majority of cases this is fine as most people deal with >batches of files from the same array design which have been produced by >computer, and so the assumption holds. However, I have come across >cases where this has certainly not been true, and I think new users of >bioconductor are maybe not aware of it. True enough. ?read.maimages has a section called "Warnings:" which cautions on exactly this point. Gordon >Mick