Arguments Details

dyebias.application.subset Return a subset of reporters that can be dye bias-corrected reasonably well Description Convenience function returning a subset of reporters that can be expected to be corrected reasonably well. Often, the logical AND of this set and that of maW(data.norm) == 1.0 is used. The resulting subset is passed as the application.subset-argument to dyebias.apply.correction. Arguments data.raw A marrayRaw object whose normalized data is to be dye bias-corrected. min.SNR The minimum signal to noise ratio to require. It is loosely defined here as the foreground over the background signal. The background signal may not be real; see below. use.background Logical indicating whether or not to use the background signals maRb(data.raw) and maGb(data.raw). If the data.raw object does not have them, specify use.background=FALSE. This will use the smallest foreground of all reporters instead of the real backgrounds. maxA The maximum signal that is still allowed. Details This routine requires an marrayRaw object since only that contains the background intensities. If you only have normalized data, use something like bg <-matrix(0.5, nrow=maNspots(data.norm), ncol=maNsamples(data.norm)) data.raw <-new("marrayRaw", maRf=maR(data.norm), maGf=maG(data.norm), maRb=bg, maGb=bg, maW=maW(data.norm)) 1 2 dyebias.apply.correction Value A matrix of logicals with the same dimensions as those of maRf{data.raw} is returned. Adaptable gene-specific dye bias correction for two-channel DNA microar-rays. Examples ## First load data and estimate the iGSDBs ## (see dyebias.estimate.iGSDBs) ### choose the estimators and which spots to correct: estimator.subset