Rathi, No, this tool doesn't deal with the .CEL files you generated from your microarray analysis, and you wont be accessing microarrayGroups.ra. That file would only be edited if you were setting up your own mirror site.
If you scroll to the bottom of our microarray wiki page, there are instructions for making a Custom Track. That's what you want. The instructions on the first part of that page have to do a different way of creating a track of microarray data in the browser. The wiki page is here: http://genomewiki.ucsc.edu/index.php/Microarray_track You'll want to have your data in the format similar to the example custom track that is provided. And yes, that means that you'll have to do some data processing to condense your raw .CEL data into an actual value per "gene" or "probe" if that's the resolution you want to look at. I hope this helps to get you started. Please let me know if you require further assistance creating your custom track. Kayla Smith UCSC Genome Bioinformatics Group ----- "Rathi Thiagarajan" <[email protected]> wrote: > Hi Jennifer, > > Thanks for the quick reply. I would prefere to use the sessions rather > > than the mirror. > > I have referred to the Microarray track Wiki page but still not sure > about > several key aspects: > > 1) do I have to physically load the .CEL files in > microarrayGroups.ra? > 2) What numbers are represented in the expScores? Can I use any > numbers > here (i.e. Fold Change) for the representation of the heatmap scale? > 3) Am I required to provide the Mean and Median? > 4) how do I get access to microarrayGroups.ra > (kent/src/hg/makeDb/hgCgiData)? Do I need to consult a UCSC mirror > administrator? > > Thanks again and looking forward to your reply. > > Cheers, > Rathi > > On Fri, 02 Oct 2009 02:26:51 +1000, Jennifer Jackson > <[email protected]> > wrote: > > > Hello, > > > > Do you want to load the data as a Custom track at UCSC (perhaps > saved in > > a Session)? Or do you want to load the data into your own mirror > > database? > > > > If a Custom track at UCSC is your goal, follow these instructions > > (below) and submit using the Custom track page. Consider using a > Session > > to save data for longer than 48hrs on the server. The wiki link that > you > > used is a great place to learn about formatting and should be > followed. > > > > > http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#CustomTracks > > http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#Sessions > > > > Thanks, Jennifer > > > > > > ------------------------------------------------ > > Jennifer Jackson > > UCSC Genome Bioinformatics Group > > > > ----- "Rathi Thiagarajan" <[email protected]> wrote: > > > >> From: "Rathi Thiagarajan" <[email protected]> > >> To: [email protected] > >> Sent: Thursday, October 1, 2009 12:19:10 AM GMT -08:00 US/Canada > Pacific > >> Subject: [Genome] Microarray track advice > >> > >> Hi there, > >> > >> I am very interested in representing the Mouse Embryonic Kidney > >> Subcompartment Microarray Atlas (Affymetrix M430.2, over 50 .CEL > >> files) > >> published in Dev. Cell in 2008 by Eric Brunskill et. al as a > >> microarray > >> track (i.e. GNF Atlas /Affy Exon track), but don't know where to > >> start. > >> > >> I have referred to the Microarray track Wiki page but still not > sure > >> about > >> several key aspects: > >> 1) do I have to physically load the .CEL files in > >> microarrayGroups.ra? > >> 2) What numbers are represented in the expScores? Can I use any > >> numbers > >> here (i.e. Fold Change) for the representation of the heatmap > scale? > >> 3) Am I required to provide the Mean and Median? > >> 4) how do I get access to microarrayGroups.ra > >> (kent/src/hg/makeDb/hgCgiData)? Do I need to a UCSC mirror > >> adminstrator? > >> > >> > >> Thanking you in advance for you advice, patience and feedback. > >> > >> Cheers, > >> Rathi > >> > >> _______________________________________________ > >> Genome maillist - [email protected] > >> https://lists.soe.ucsc.edu/mailman/listinfo/genome > > -- > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
