Hello Kishore, For microarray tracks, we display a single color when the track is in dense mode. Here is a Genome Browser session that shows the type of tracks I am talking about:
http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=Rhead&hgS_otherUserSessionName=MLQ_kishore Are you asking how we decide what color to display when a mircroarray custom track is set to visibility dense? If so, I can tell you that the display in dense mode is the same as the brightest tissue (in either red or green) for each probe. We don't display the mean or median value, because that would cause most tracks to display in black and not convey any useful information. If I have misinterpreted your question, you might be able to find the answer you were looking for on this page in our genomewiki (note the custom track specific information at the bottom of the page): http://genomewiki.ucsc.edu/index.php/Microarray_track If you still have questions, please feel free to contact us again at [email protected]. -- Brooke Rhead UCSC Genome Bioinformatics Group On 01/27/09 08:52, kishore wrote: > Dear UCSC staff, > i created some microarray custom tracks in the UCSC genome browser. since i have a lot of samples i am using the "DENSE" view feature for the tracks instead of the "FULL" view. in the dense view format, it gives me the expression/intensity values from the microarray as horizontal heat map bars. however, i could not find a heat map bar that corrsponds to the approximate expression values for the different shades of gray. is there a way that i can get a heat map bar corresponding to the expression values that i put in?? thanks in advance > > Kishore Guda, BVSc&A.H (DVM)., Ph.D. > Case Western Reserve University-Ireland Cancer Center > Cleveland, OH 44106 > > > > _______________________________________________ > Genome maillist - [email protected] > http://www.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] http://www.soe.ucsc.edu/mailman/listinfo/genome
