Hi, I am comparing results from the 1.4 Bioconductor release version of GCRMA with the old release 1.3 version. Plotting the density of expression values results in a bi-modal distribution in both versions. However, with the old version the largest peak was at low intensities and there was a smaller (~1/3) peak at higher intensities. But with the new version, the largest peak is at high intensities and the smaller peak is at low intensity. Biologically, the old results make much more sense (only about 1/3 of the genes should express in the spinal cord). What has happened to the code of GCRMA to make the differences? Best wishes and thanks to all involved in gcrma. Harry -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~ Dr Andrew Harrison Tel: 44 (0) 207 679 3890 Biomolecular Structure and Modelling Unit Fax: 44 (0) 207 679 7193 Biochemistry and Molecular Biology Dept. University College London Gower Street Email: harry@biochem.ucl.ac.uk London, WC1E 6BT, UK http://www.biochem.ucl.ac.uk/~harry ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~