Problem loading microarray track in local UCSC

[Aarthi Mohan]

Hi,

I am trying to setup microarray tracks in my local UCSC installation. I followed the instruction on this wiki http://genomewiki.ucsc.edu/index.php/Microarray_track.

I still get this error  'hashMustFindVal: 'array' not found', when trying to view that track

I followed these steps:

1. Added track details in trackDb.ra file

2. Added groupings details in microarrayGroups.ra file and placed it under my organism directory (under hgCgiData) and run make

3. Loaded the bed15 files using hgLoadBed

4. Run hgTrackDb 

trackDb.ra file:

track rnapol2_array

shortLabel rnapol2_CHIP

longLabel rnapol2 intragenic and intergenic probes

group regulation

priority 79.1

visibility hide

type expRatio

expScale 3.0

expStep 0.5

groupings array

microarrayGroups.ra file:

name array

type groupings

all exp_foldchange

name exp_foldchange

type all

description treat vs ctrl foldchange

expIds 0,1,2,3,4,5,

groupSizes 1,1,1,1,1,1,

names TP1,TP2,TP3,TP4,TP5,TP6,

microarray_file:

#chrom chromStart chromEnd name score strand thickStart thickEnd reserved blockCount blockSizes chromStarts expCount expIds expScores

chr1 477429 477499 ac1rRNA28s_0 42 + 477429 477499 0 1 70, 0, 6 0,1,2,3,4,5, -0.459025411667,-0.432431992667,-0.254639977333,-0.549278988,-0.200176743,-0.160042251,

chr1 479408 479478 ac1rRNA28s_1 42 + 479408 479478 0 1 70, 0, 6 0,1,2,3,4,5, 2.920002221,3.32211873533,4.21103540667,4.17879635133,2.96150068333,3.28662271933,

Appreciate your help. 

Thanks!

Aarthi

[Steve Heitner]

Hello, Aarthi.

From what you describe, it does seem like this should be working.  I’m assuming you’ve already checked these, but a couple of things you might want to check:

1. Check the spelling and capitalization of your /hgCgiData/$organism directory.  It should match what is in your hgcentral.dbDb entry for this organism.

2. When you run a make, it should copy your /hgCgiData/$organism/microarrayGroups.ra file to /usr/local/apache/cgi-bin/hgCgiData/$organism.  Check to make sure this file exists there.  If not, this is definitely a problem.

We can start from here and if this doesn’t solve the problem, we can delve deeper.

Please contact us again at gen...@soe.ucsc.edu if you have any further questions.  All messages sent to that address are archived on a publicly-accessible Google Groups forum.  If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

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Steve Heitner
UCSC Genome Bioinformatics Group

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[Aarthi Mohan]

Hi Steve,

Thanks for the help. Good catch, the error was indeed with the conflict of name between the organism folder under hgCgiData and the hgcentral.dbDb database entry. 

I would also like to know what the expScale  should we use. I have CHIP data for 6 time points, and should it represent min, max from all CHIP or time-point min, max. Because, I see all reds and greens for many probes, there is no change between time-points. 

Thanks,

Aathi

[Matthew Speir]

Hi Aarthi,

You can find more information on the "expScale" setting under the "trackDb" settings of the "Microarray Track" genomewiki page: http://genomewiki.ucsc.edu/index.php/Microarray_track#trackDb_Settings:

• expScale -- an absolute value that reflects the dynamic range of the data and influences the coloring of the track. For example, an expScale setting of 3.0 indicates that most of the data lie between -3.0 and 3.0; the brightest green will be used for values less than or equal to -3.0 and the brightest red for values greater than or equal to 3.0.

You will need to look at your data and make a determination as to what expScale value works for your various data sets.

I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible Google Groups forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

Matthew Speir
UCSC Genome Bioinformatics Group

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