We're using marrayNorm to normalize our data, and we'd like to normalize with respect to pin-tips as well as arrays. However, our choices include plate normalization. Can someone describe the difference between pin-tip and plate normalization (is it possible that we only have pin-tip issues and not plate issues?) Additionally, does marrayNorm have a global normalization? And is global normalization synonymous with array normalization? Thanks, Jo Jo Hardin Assistant Professor Department of Mathematics Pomona College 610 N. College Ave. Claremont, CA 91711 909-607-8717 jo.hardin@pomona.edu [[alternative HTML version deleted]]

Hi Johanna, print-tip and plate are usually "orthogonal" factors, in the following sense: print-tip corresponds to spatial sectors on the array, whereas plate corresponds to the 384- or 96-well plates in which the DNA was PCR amplified, stored, and brought to the spotter. Often you can visually identify plate effects as gradients or particularly bright or dark rows within a sector. Whether the plate effects are technical noise that needs to be normalized away, or whether they are true biological signal depends very much on the experiment - often, different plates correspond to different clone libraries e.g. from different tissues. marray (and may I note vsn as well) currently allow only estimation of either print-tip or plate effects. But one could imagine a (generalized) linear model that fits both, just nobody seems to have implemented this yet - or has anyone? Best wishes Wolfgang Johanna Hardin wrote: > We're using marrayNorm to normalize our data, and we'd like to normalize > with respect to pin-tips as well as arrays. However, our choices > include plate normalization. Can someone describe the difference > between pin-tip and plate normalization (is it possible that we only > have pin-tip issues and not plate issues?) > > > > Additionally, does marrayNorm have a global normalization? And is > global normalization synonymous with array normalization? > > > > Thanks, Jo > > > > Jo Hardin > > Assistant Professor > > Department of Mathematics > > Pomona College > > 610 N. College Ave. > > Claremont, CA 91711 > > 909-607-8717 > > jo.hardin@pomona.edu > > > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor -- Best regards Wolfgang ------------------------------------- Wolfgang Huber European Bioinformatics Institute European Molecular Biology Laboratory Cambridge CB10 1SD England Phone: +44 1223 494642 Fax: +44 1223 494486 Http: www.ebi.ac.uk/huber