Hi, Using the hard-coded version of rma in the library affy, I find the expression values to be on a quite narrow range in relative terms (range=(3.5,14)). With other methods (eg mas, dchip), the signals span about four order of magnitude. Does this mean the expressions output by rma are log-tranformed? if so, which basis should be used to recover non-transformed signals? Thank you Martino --------------------------------------- Martino Barenco CoMPLEX 4, Stephenson Way London NW1 2HE Tel.: +44 20 7679 5088 Fax.: +44 20 7383 5519 Email: m.barenco@ucl.ac.uk

RMA expression measures are log base 2 scale (as given both via rma() and expresso()). If you wish to have non transformed signals use take 2 to the power of your expression measures. ie something like 2^(exprs(eset)) On Wed, 2003-05-21 at 03:33, Martino Barenco wrote: > Hi, > > Using the hard-coded version of rma in the library affy, I find the > expression values to be on a quite narrow range in relative terms > (range=(3.5,14)). With other methods (eg mas, dchip), the signals span > about four order of magnitude. Does this mean the expressions output by > rma are log-tranformed? if so, which basis should be used to recover > non-transformed signals? > > Thank you > > Martino > --------------------------------------- > Martino Barenco > CoMPLEX > 4, Stephenson Way > London NW1 2HE > Tel.: +44 20 7679 5088 > Fax.: +44 20 7383 5519 > Email: m.barenco@ucl.ac.uk > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor -- Ben Bolstad <bolstad@stat.berkeley.edu>