Jim et al, > The probe sequence files for the Gene microarrays are slightly different > from the previous generation 3' biased arrays, so this will require some > modification of the matchprobes package to accommodate the differences. > > Making the changes is actually trivial - the makeProbePackage() function > will use an arbitrary function (called via the 'importfun' argument) to > read in the data from a probe_tab file. If one wanted a probe package > that is exactly the same as what we currently supply, you could modify > the existing function readProbeDataAffy() to read in the extra columns > in the file and then just discard them. > > The question then remains; is this a good idea or not? I'm not sure it > is, and I think we need to think about these new chips a bit to decide > what the probe package should contain. > > For instance, the sequences that they report are the reverse complement > of the target sequences. I'm not sure what the sequences for the 3' > biased arrays were, but we might want to make what is in the package > consistent (or maybe not - new chip == new package?). > > In addition, there are no MM probes on these chips. Instead there are > just a bunch of control probes: > > The usual AFFX probes > A chip control > Antigenomic background probes > Genomic background probes > Exonic normalization control probes > Intronic normalization control probes > Unmapped probes Ahh.. this is all new information to me.. I probably should have read the Affy site a little closer :/ > Since there are no MM probes, these packages clearly won't be useful for > gcrma(), so what are the use cases for the package? This is what will > inform any further discussion. I think this is where I immediately fell down with my handling of things - I assumed they were just a subset of the exon array or related to the hgfocus arrays, but with a 'traditional' Affy setup - obviously not. I'll go back to the data and decide what I need before further comment.. Thanks! Dan -- Bioinformatics Support Unit || http://bsu.ncl.ac.uk/ Institute for Cell and Molecular Biosciences, Faculty of Medical Sciences, Framlington Place, Newcastle University, Newcastle, NE2 4HH Tel: +44 (0)191 222 7253 (Leech offices: Rooms M.2046/M.2046A - Mon/Wed) Tel: +44 (0)191 246 4833 (Devonshire offices: Rooms G.25/G.26 - Thu/Fri)