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 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
