[Genome] affyHumanExon

[Archana Thakkapallayil]

Hello Jared,

You can get more details about any track in the browser by clicking on 
the blue or gray mini-button to the left of the track in the display, or 
by pressing the hyper link in the Track Controls (in this case "Affy All 
Exon").  The description page will describe the track, the methods used 
to create the track, the credits and the references.

Here's an excerpt from the description page for the Affy All Exon track 
(for the latest human assembly: hg18):

RNA (from a commercial source) from 11 tissues were hybridized to 
Affymetrix Human Exon 1.0 ST arrays. For each tissue, 3 replicate 
experiments were done for a total of 33 arrays. The arrays' raw signal 
intensity was normalized with a quantile normalization method, then run 
through the PLIER algorithm. The normalized data were then converted to 
log-ratios, which are displayed as green for negative log-ratios 
(underexpression), and red for positive (overexpression).

I hope this information is helpful to you. If your questions aren't 
answered after reading the description page, please feel free to write 
back to the list

Regards,

Archana
UCSC Genome Bioinformatics Group

Bischof, Jared wrote:
> Also, are the expScores values in the "affyHumanExon" table the raw values?  Or are they the values after normalization and conversion to log-ratios?
>
>
> -----Original Message-----
> From: Bischof, Jared 
> Sent: Mon 10/29/2007 11:35 PM
> To: genome at soe.ucsc.edu
> Subject: affyHumanExon
>  
> Do the visual (red/green) representations of the arrays in the "Affymetrix All Exon Chips" track represent the median value of the 3 replicate experiments for each probe?  Or is it the mean or something else?
>
> -Jared Bischof
>
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