Hello Xinwei, You will need 2 tables to compile a list of expression values for the cortex and then the best method for determining an appropriate cutoff value will be at your discretion. For an explanation of the two tables and how to parse them to retrieve your values of interest please see this previously answered mailing list question:
http://www.soe.ucsc.edu/pipermail/genome/2006-August/011453.html This question describes the analogous tables for human and for mouse you will want the tables: gnfMouseAtlas2Median (in the hgFixed database) gnfAtlas2 (in the mm9 [mouse] database) To get the first table from the table browser choose: group: All tables database: hgFixed table: hgFixed.gnfMouseAtlas2Median The second table can be found the usual way by selecting: genome: Mouse assembly: July 2007 track: GNF Atlas 2 table: gnfAtlas2 Hopefully this information was helpful and answers your question. If you have further questions or require clarification feel free to contact the mailing list at [EMAIL PROTECTED] Regards, Pauline Fujita UCSC Genome Bioinformatics Group http://genome.ucsc.edu Xinwei Han wrote: > Hello, > > Sorry to disturb. I am studying gene expression in mouse and today I > downloaded "GnfMouseAtlas2median" file from table browser. By reading > previous threads, I found the last column is the so-called average > difference value from affymetrix. I want to find out whether several > genes express in cortex or not. Then which value should I use as the > cutoff to distinguish "expressing in cortex" and "not expressing in > cortex" ? > > One previous thread also mentioned average difference value could be > negative values. But in this file, it seemed that all average difference > values are positive. Could you tell me the reason? > > Thank you! > > Best regards, > Xinwei Han > _______________________________________________ > Genome maillist - [email protected] > http://www.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] http://www.soe.ucsc.edu/mailman/listinfo/genome
