affymetrix probeset track info

[matt arno]

Hi - I'm looking at the way Affy probesets/transcript clusters are arranged as a track on the human genome browser and one of the configuration options is:

Show only items with score at or above: (0 - 1000)

What exactly does this score relate to? Also some of the probesets are duplicated in the browser which can be confusing; is there any valid reason for this?

Cheers,

Matt

[Brooke Rhead]

Hi Matt,

Can you clarify which track you are referring to? I don't see the score
configuration option on any of these tracks (in the Expression track
group on the GRCh37/hg19 browser):

Affy Exon Array
Affy GNF1H
Affy RNA Loc
Affy U133
Affy U133Plus2
Affy U95

Let us know which track you are looking at, and we can help figure out
the answer. In general, the score (between 0-1000) is what determines
how darkly an item is displayed in the browser (with 1000 being black).
The score for any given track is often calculated by the data
provider, so you might need to contact them directly with questions
about what it represents.

For the duplicated probesets, do you mean they are duplicated in a
single track, or across more than one track? Can you give us an example?

Please reply to gen...@soe.ucsc.edu.

--
Brooke Rhead
UCSC Genome Bioinformatics Group

On 3/20/13 10:39 AM, matt arno wrote:
> Hi - I'm looking at the way Affy probesets/transcript clusters are
> arranged as a track on the human genome browser and one of the
> configuration options is:
>

> *Show only items with score at or above: (0 - 1000)*
> *
> *
> *What exactly does this score relate to? Also some of the probesets are

> duplicated in the browser which can be confusing; is there any valid

> reason for this?*
> *
> *
> *Cheers,*
> *Matt*
>
> --
>
>
>

[matt arno]

Dear Brooke - thanks for the reply. I got to the track using a link straight from the Affy database (NetAffx) - it looks like it's applying a BED file from Affy (which tallies with what you said below). Could you have a look and see if it's a UCSC score or an Affy score? When I change the score (e.g. to 500) then a lot of the aligned probesets disappear from the track; it could be some kind of evidence or annotation threshold?

You will also see the duplicated probesets (within the same track)

http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&position=chr6:51954308-52055436&hgt.customText=http://www.affymetrix.com/analysis/downloads/expression_array_bed_files/HuEx-1_0-st-v2.hg19.chr6.bed.gz

Many thanks,

Matt

[Brooke Rhead]

Hi Matt,

I see now. The links from Affymetrix load four custom tracks into the
Genome Browser (they show up in the track controls under the group
"other" at the bottom of the page). You will need to contact Affy
directly about the contents of the tracks, since we don't actually host
the data here.

--
Brooke Rhead
UCSC Genome Bioinformatics Group

On 3/22/13 2:32 AM, matt arno wrote:
> Dear Brooke - thanks for the reply. I got to the track using a link
> straight from the Affy database (NetAffx) - it looks like it's applying
> a BED file from Affy (which tallies with what you said below). Could you
> have a look and see if it's a UCSC score or an Affy score? When I change
> the score (e.g. to 500) then a lot of the aligned probesets disappear
> from the track; it could be some kind of evidence or annotation threshold?
>
> You will also see the duplicated probesets (within the same track)
>
>
> http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&position=chr6:51954308-52055436&hgt.customText=http://www.affymetrix.com/analysis/downloads/expression_array_bed_files/HuEx-1_0-st-v2.hg19.chr6.bed.gz
>
> Many thanks,
> Matt
>
>
> On 21 March 2013 22:52, Brooke Rhead <rh...@soe.ucsc.edu

> <mailto:rh...@soe.ucsc.edu>> wrote:
>
> Hi Matt,
>
> Can you clarify which track you are referring to? I don't see the
> score configuration option on any of these tracks (in the Expression
> track group on the GRCh37/hg19 browser):
>
> Affy Exon Array
> Affy GNF1H
> Affy RNA Loc
> Affy U133
> Affy U133Plus2
> Affy U95
>
> Let us know which track you are looking at, and we can help figure
> out the answer. In general, the score (between 0-1000) is what
> determines how darkly an item is displayed in the browser (with 1000
> being black). The score for any given track is often calculated by
> the data provider, so you might need to contact them directly with
> questions about what it represents.
>
> For the duplicated probesets, do you mean they are duplicated in a
> single track, or across more than one track? Can you give us an
> example?
>

> Please reply to gen...@soe.ucsc.edu <mailto:gen...@soe.ucsc.edu>.