Dear list, 1) I wrote a couple of functions to remove a list of probes and/or probesets from a given CDF and Probe environments (I did not find that anywhere). The idea is to be able to remove 'offending' probes from rma and gcrma calculations. These functions are included in the attached file 'removeProbes.R', and an example is included in 'removeProbesEx.R'. The code is there to anyone that want to give it a try. 2) The function 'RemoveProbes' modifies the specified CDF and PROBE environments in a consistent way. IMHO this should be gcrma-compliant (i am using gcrma 1.1.3) . However I found a strange behavior I would like to discuss. If just a single probe is removed (e.g '1000_at1' from Dilution dataset, see removeProbesEx.R) then only the RMA expression value of the modified probeset changes when compared with the full-probe result :-) . The same is true for GCRMA 1.1.0. However, the expression values of many different probe-sets (and not only the modified one) calculated by GCRMA 1.1.3 change (see figure attached where expression values calculated with and without 1000_at1 are plot for both, RMA and GCRMA ). After some analysis I think the problem is in the function 'bg.parameters.ns' of gcrma 1.1.3. The sampling of 5000 affinity values performed in order to fit the MM-affinities dependency produce slightly different results when the number of sampled affinities changes (even in one unit!). This results in different loess fitting curves, and different mean and sigma estimates for PM nonspecific signals, etc, etc. On the contrary the method to estimate bg parameters implemented in version 1.1.0 (based on the analysis of PM distribution, group by affinities) seems to be far most robust. ( of course I am talking here of implementation, not on the different working hypothesis) . I would like to here opinions regarding how this behavior affect gcrma estimates? Should one for instance conclude that this instability precludes accuracy in version 1.1.3? Regards, -------------- next part -------------- A non-text attachment was scrubbed... Name: oneout.png Type: image/png Size: 5236 bytes Desc: not available Url : https://stat.ethz.ch/pipermail/bioconductor/attachments/20050420 /2a5bc8c1/oneout.png -------------- next part -------------- Ariel Chernomoretz, Ph.D. Centre de recherche du CHUL 2705 Blv Laurier, bloc T-367 Sainte-Foy, Qc G1V 4G2 (418)-525-4444 ext 46339