vsn

The function calibrates for sample-to-sample variations through shifting and scaling, and transforms the intensities to a scale where the variance is approximately independent of the mean intensity. The variance stabilising transformation is equivalent to the natural logarithm in the high-intensity range, and to a linear transformation in the low-intensity range. In an intermediate range, the arsinh function interpolates smoothly between the two. The parameters are estimated through a robust variant of maximum likelihood. This assumes that for the majority of genes the expression levels are not much different across the samples, i.e., that only a minority of genes (less than a fraction '1-lts.quantile') is differentially expressed [6,7].

NOTE: For this option the input object should contain raw intensities, i.e., prior to background correction, log-transformation or any normalisation. (I.e the RG object returned from the gprload or AgilentLoad nodes).



Bjørn Kåre Alsberg 2006-04-06