Hello, I have started using bioconductor (which is great, by the way), and I have a question regarding how to choose a minimum expression threshold. I have read in the Affymetrix cel files, calculated expression using rma(), and now have a data frame with ~22k expression values across 14 samples (using the U133A chip). There are expression values for each Affy spot - although it is probably not true that this tissue expresses all 22k genes. My question is how do I choose a threshold above which I consider the gene to be expressed? In addition (please correct me if I'm wrong), using only the number of expressed genes (or at least not all of the spots) will make for better values using the multtest package. Can someone point me in the right direction, or point out some good references on this topic? Thanks.

hi! i dont know of any good references. in practice i dont like to arbitrarily decide on a such cut-offs. this could be very problematic if you use MAS 5.0, but with other expression measures such as pm only li wong and rma you usually dont need this filtering step. sorry i cant be of more help, rafael On Tue, 26 Aug 2003, Bob wrote: > Hello, > I have started using bioconductor (which is great, by > the way), and I have a question regarding how to > choose a minimum expression threshold. > > I have read in the Affymetrix cel files, calculated > expression using rma(), and now have a data frame with > ~22k expression values across 14 samples (using the > U133A chip). There are expression values for each > Affy spot - although it is probably not true that this > tissue expresses all 22k genes. My question is how do > I choose a threshold above which I consider the gene > to be expressed? > > In addition (please correct me if I'm wrong), using > only the number of expressed genes (or at least not > all of the spots) will make for better values using > the multtest package. > > Can someone point me in the right direction, or point > out some good references on this topic? > > Thanks. > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor >