[Genome] affyHumanExon

[Andy Pohl]

By default it's the median, but you can also select the mean or just
show all the replicates (they are suffixed with _A, _B, or _C).  The
data is a log-ratio recommended by Affymetrix and not raw.  I'd be
happy to help you further.  We have the pre-log-ratio'd data, but not
completely raw.  Affymetrix only provided data cooked slightly with
the PLIER algorithm (to normalize).

Andy Pohl
CBSE

On 10/30/07, Jared Bischof <jbischof at childrensmemorial.org> wrote:
> Thanks Archana, but I already looked at that and it didn't answer my
> questions.  Which value is being represented by the expression color?  Is it
> the median value of the three experiments for each tissue?
>
> And, are the values in the affyHumanExon table the raw values, or are they
> the values after normalization and conversion to log-ratios?
>
> -Jared
>
>
> > From: Archana Thakkapallayil <archanat at soe.ucsc.edu>
> > Reply-To: <archanat at soe.ucsc.edu>
> > Date: Tue, 30 Oct 2007 09:24:42 -0700
> > To: "Bischof, Jared" <JBischof at childrensmemorial.org>
> > Cc: <genome at soe.ucsc.edu>
> > Subject: Re: [Genome] affyHumanExon
> >
> > 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
> >>
> >> _______________________________________________
> >> Genome maillist  -  Genome at soe.ucsc.edu
> >> http://www.soe.ucsc.edu/mailman/listinfo/genome
> >>
>
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