Hi all, I d like to know if there is a package in BioC that can identify genes that are differentially expressed between 2 conditions and analyze their distribution along the chromosomes to say if their distribution is random or if it has a non random distribution with some sort of clusters in some part of the chromosomes... for instance, a tool that could help to detect translocations, loss or gain of chromosomes from the microarray data... thanks Philippe [[alternate HTML version deleted]]

Phguardiol@aol.com writes: > I d like to know if there is a package in BioC that can identify genes that > are differentially expressed between 2 conditions and analyze their > distribution along the chromosomes to say if their distribution is random or > if it has a non random distribution with some sort of clusters in some part > of the chromosomes... for instance, a tool that could help to detect > translocations, loss or gain of chromosomes from the microarray data... > thanks You can do it, but I think you are talking about at least 2 packages, assuming that you are using annotated gene expression arrays, and you need to define (and possibly program up) specifically what you mean by "differential". There are at least 10 specific definitions, if not hundreds more possible. best, -tony -- A.J. Rossini rossini@u.washington.edu http://software.biostat.washington.edu/ Biostatistics, U Washington and Fred Hutchinson Cancer Research Center FHCRC:Tu: 206-667-7025 (fax=4812)|Voicemail is pretty sketchy/use Email UW: Th: 206-543-1044 (fax=3286)|Change last 4 digits of phone to FAX They make me add this: CONFIDENTIALITY NOTICE: This e-mail message and any attachments may be confidential and privileged. If you received this message in error, please destroy it and notify the sender. Thank you.

Phguardiol@aol.com <phguardiol@aol.com> [Wed, Apr 09, 2003 at 03:19:00PM CEST]: > Hi all, > I d like to know if there is a package in BioC that can identify genes that > are differentially expressed between 2 conditions and analyze their > distribution along the chromosomes to say if their distribution is random or > if it has a non random distribution with some sort of clusters in some part > of the chromosomes... for instance, a tool that could help to detect > translocations, loss or gain of chromosomes from the microarray data... I have worked a bit on it; you can read about it on http://www.panix.com/~derwisch/hannes/longrun. There is some code about the longest run statistic and the scan statistic, which you might find useful if you dichotomize the differentially expressed genes. As others have pointed out, this is only one possibility where non-randomness comes in. Cheers Johannes -- Johannes H?sing There is something fascinating about science. One gets hannes@ruhrau.de such wholesale returns of conjecture from such a trifling investment of fact. Mark Twain

You might like to look at: 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 where we use Affy *expression* arrays to detect deletions and 'SFP's - "single feature polymorphisms" There is a download page at http://naturalvariation.org/sfp that has R scripts that we used. Chuck On Wed, 9 Apr 2003 Phguardiol@aol.com wrote: > Hi all, > I d like to know if there is a package in BioC that can identify genes that > are differentially expressed between 2 conditions and analyze their > distribution along the chromosomes to say if their distribution is random or > if it has a non random distribution with some sort of clusters in some part > of the chromosomes... for instance, a tool that could help to detect > translocations, loss or gain of chromosomes from the microarray data... > thanks > Philippe > > [[alternate HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor > 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 92093-0645