Oops! minor correction below On Thu, 9 Dec 2004, Charles C. Berry wrote: > > > Mark, > > In > > Borevitz, J.O., Liang, D., Plouffe, D., Chang, H., Zhu, T., Weigel, D., > Berry, C.C., Winzeler, E., and Chory. J. (2003) Large Scale Identification of > Single Feature Polymorphisms in Complex Genomes Genome Research 13,513-523. > > we used individual probesets on Affy arrays to search for polymorphisms among > inbred strains (hyb'ing genomic DNA rather than RNA). > > A collection of the tools we used to identify probesets and/or regions that ................................................^^^^^^^^^... I meant individual probes, not probesets. > differentially bind according to strain may be found at: > > http://naturalvariation.org/sfp > > and the 'Methods' link will connect you to some newer work and scripts. > > ---------- > > Although you seem to have somewhat different objectives, it looks like > similar statistical tools would apply to your situation. > > Chuck > > > On Thu, 9 Dec 2004, Kimpel, Mark W wrote: > >> My apologies to those with far more statistical expertise than I, but I >> have what may (or may not) be a straightforward question. >> >> After performing SAM analysis of an experiment comparing two strains of >> rats, I have a list of about 200 significant affy rat probesets (genes) >> that I have mapped to their chromosomal locations. Some of the genes >> appear to cluster into discrete physical chromosomal regions, which I >> suspect is related to underlying genetic differences between the two >> inbred strains. Based on their chromosomal location, I have clustered >> these significant genes into discrete bins. Something thing to remember >> when solving this problem is that the distribution along chromosomes of >> all affy rat probesets is not uniform. Thus my fear that some of the >> granularity of the chromosomal locations of significant genes could not >> only be due to chance, but to granularity of the underlying distribution. >> >> At this point I would like to test: >> >> 1. if the distribution of sig. genes amongst the bins is >> statistically different from that of the population of all affy >> genes from which they were drawn. >> 2. if the above distribution of sig genes is, as I suspect >> different, which of the bins are responsible for this significant >> difference. It would be great to assign significance p values to >> the significance of each bin. >> >> I believe this is similar to the problem faced in analyzing the >> distribution of genes in GO categories but I am not familiar with the >> proper solution. >> >> Any sample code would be greatly appreciated. For an example, assume that >> I have two matrices, each of two columns with genes represented by rows. >> The first column is the probeset ID, the second column the "bin" that it >> falls into. One matrix is of all rat affy genes, the second on is only >> the significant genes. >> >> Thanks, >> >> Mark W. Kimpel MD >> >> Department of Psychiatry >> Indiana University School of Medicine >> Biotechnology, Research, & Training Center >> 1345 W. 16th Street >> Indianapolis, IN 46202 >> >> >> > > Charles C. Berry (858) 534-2098 > Dept of Family/Preventive Medicine > E mailto:cberry@tajo.ucsd.edu UC San Diego > http://hacuna.ucsd.edu/members/ccb.html La Jolla, San Diego 92093-0717 > > Charles C. Berry (858) 534-2098 Dept of Family/Preventive Medicine E mailto:cberry@tajo.ucsd.edu UC San Diego http://hacuna.ucsd.edu/members/ccb.html La Jolla, San Diego 92093-0717