Hi there: suppose i have some arrays and their log10(intensities) have been made into a data.frame of probe X sample; I am wondering for that case, is there some normalization function available in BioC for that? I do not have other info like background info so I think I cannot run something like justRMA since it is a wrapper. My question is, if I want to do rma normalization only, is there a way to do that? I feel sometimes it is good to have a wrapper function; but sometimes I would rather have some basic functions so that I can customerize the pipeline. Best, -- Weiwei Shi, Ph.D Research Scientist GeneGO, Inc. "Did you always know?" "No, I did not. But I believed..." ---Matrix III

Depending on how or what your data is you may or may not be able to do the full RMA. Since you don't seem to have CEL files I am guessing that you may not have Affymetrix data, and then the full algorithm might not be applicable. That said all the parts are exposed in one way or another. For the background correction, see bg.adjust() in affy for quantile normalization see normalize.quantiles() in preprocessCore For the median polish summarization, see subColSummarizeMedianpolish() in preprocessCore On Fri, 2007-11-23 at 16:37 -0500, Weiwei Shi wrote: > Hi there: > > suppose i have some arrays and their log10(intensities) have been made > into a data.frame of probe X sample; > > I am wondering for that case, is there some normalization function > available in BioC for that? I do not have other info like background > info so I think I cannot run something like justRMA since it is a > wrapper. My question is, if I want to do rma normalization only, is > there a way to do that? > > I feel sometimes it is good to have a wrapper function; but sometimes > I would rather have some basic functions so that I can customerize the > pipeline. > > Best, >