Hi Kishore, We now have a grayscale color key for BED tracks at: http://genome.ucsc.edu/FAQ/FAQformat#format1
and at: http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#TRACK -- Brooke Rhead UCSC Genome Bioinformatics Group On 01/28/09 10:54, kishore wrote: > dear brooke, > thanks for your prompt reply. may be i didn't explain the question > properly. suppose i have 5 samples with an arbitrary microarray > expression values for a given gene of 150, 270, 380, 590 and 1500. now > when i use the "dense" function i will get the horizontal bar for these > five samples in shades of gray with the intensity of the grey > corresponding to the numerical values. for example, the sample with > a value of 1500 will be more darker than the sample with a value of 590 > and so on and so forth. am i interpreting this so far correctly?? now > what i am asking is whether there is a small key "shades of grey" > bar image that actually gives me the approximate numerical value range > for each shade of grey. thanks in advance. > > > > Kishore Guda, BVSc&A.H (DVM)., Ph.D. > Case Western Reserve University-Ireland Cancer Center > Cleveland, OH 44106 > > > ------------------------------------------------------------------------ > *From:* Brooke Rhead <[email protected]> > *To:* kishore <[email protected]> > *Cc:* [email protected] > *Sent:* Tuesday, January 27, 2009 8:51:31 PM > *Subject:* Re: [Genome] custom track > > 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 > > <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] <mailto:[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] <mailto:[email protected]> > > http://www.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] http://www.soe.ucsc.edu/mailman/listinfo/genome
