Talk:Microarray track: Difference between revisions
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From the Affy HuEx 1.0 track description:<br> | From the Affy HuEx 1.0 track description:<br> | ||
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. | 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. | ||
<h3>track type error</h3> | |||
Hi again. | |||
<br>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 | |||
<br>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 | |||
<br>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. | |||
<br>Thanks again! -Matt | |||
Revision as of 02:58, 30 April 2008
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.
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
