Talk:Microarray track

Question:

What does the "score" field do in a microarray track? Thanks!

Answer:

For most microarray tracks, the "score" field is ignored. Usually all lines in a microarray table have a place-holder value of 1000 in the "score" field. (A place-holder is necessary for BED-formatted data.) The example data happens to be from the hg18 "Affy All Exon" track, which has a companion track, "Affy HuEx 1.0". The scores (of 200, 300, 500, etc.) are used in the companion track to color the probe sets displayed.

From the Affy HuEx 1.0 track description:
Probe sets are colored by class with the Core probe sets being the darkest and the Full being the lightest color. Additionally, probe sets that do not overlap the exons of a transcript cluster, but fall inside of its introns, are considered bounded by that transcript cluster and are colored slightly lighter. Probe sets that overlap the coding portion of the Core class are colored slightly darker.

Q: track type error

Hi again.
1. I'm getting an error I can't figure out: Unrecognized format type=array line 2 of http://pantheon.yale.edu/~mbj7/SestanBED15test.txt
Here's the link to my file: http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg18&position=chr1:1004629-1100379&hgt.customText=http://pantheon.yale.edu/~mbj7/SestanBED15test.txt
2. What file format do you use for BED files? I've formatted my data in Excel and saved as tab delim, but this seems to add characters that cause problems. Any advice would be greatly appreciated.
Thanks again! -Matt

A: track type error

I looked at your file at the URL you provided. If you scroll all the way to the right (keep scrolling, it's a long way!), you will see some garbage characters on lines 2, 3, and 4.

"NUM!
"DIV/0!
0

These were likely introduced by your export from Excel. These are the characters that are causing the problem. I would suggest that you try to save your file in a different format (play around with Excel -- try space-delimited or some other options), then try it again in the genome browser.

D'oh! Thanks. I copied the data from excel and just pasted into notepad and that worked great.

Question: About microarrayGroups.ra file

I am trying to display micro array tracks.
In the trackDb.ra, I have indicated the line "groupings affyAthGroups".

The contents of microarrayGroups.ra is

name affyAthGroups
type groupings
all affyAthAll

name affyAthAll
type all
description All Arrays
expIds 0
groupSizes 1,
names affyPEGexp,

However when I try to display the tracks, the browser complains,
"affyAthGroups not found"

Do I need to do any other configuration? Thanks.
-sridhar