[BioC] SCAN.UPC vs NUSE

[Peterson, Leif]

Hi Steve,

Thanks for the rapid response.  We may be able to fit in a small sub-analysis into a student thesis project - and will definitely get back to you if we pursue that.  Certainly, the outlier probesets in arrays with artifacts will have quite large or near-zero intensity levels - which when transformed into z-scores will bias the z's of all the other probesets due to their influence on the mean over all probesets.  Once we
identify those probesets, we can go into the SCAN expression set to see what happened to them. 

For now, we'll stick with removal of bad arrays based on NUSE results.

Best, Leif

Sent from my iPhone

On Sep 25, 2013, at 7:17 AM, "Steve Piccolo" <stephen.piccolo at hsc.utah.edu> wrote:

> Hi Leif,
> 
> Thanks for your email. We have not yet done a formal evaluation to address
> how well SCAN.UPC can address artifacts and degraded hybridization, etc.
> So for the time being we would recommend that you use NUSE and/or other
> quality-control tests before applying SCAN.UPC. However, when summarizing
> at the gene/probeset level, we use a 10% trimmed mean, so this may be
> adequate in many cases for excluding outlier probes due to streaks,
> blotches, etc.
> 
> We have considered to use the signal-to-noise ratio or some other metric
> that can be derived from the SCAN.UPC calculations as a way to measure
> sample quality. But so far we haven't implemented that.
> 
> If by chance you decide to do a formal evaluation along these lines, we'd
> be happy to discuss it with you.
> 
> Thanks,
> -Steve
> 
> 
> 
> On 9/25/13 4:00 AM, "bioconductor-request at r-project.org"
> <bioconductor-request at r-project.org> wrote:
> 
>> Message: 20
>> Date: Tue, 24 Sep 2013 07:55:34 -0500
>> From: "Leif Peterson" <leifepeterson at sbcglobal.net>
>> To: <bioconductor at r-project.org>
>> Subject: [BioC] SCAN.UPC vs NUSE
>> Message-ID: <001801ceb925$5cdd0440$16970cc0$@sbcglobal.net>
>> Content-Type: text/plain
>> 
>> Prior to using SCAN.UPC and ComBat, we originally ran NUSE (in AffyPLM)
>> and
>> removed Affy Hu-133A arrays for which the NUSE criterion was > 1.05.   We
>> are wondering whether use of SCAN.UPC without pre-filtering by NUSE would
>> be
>> sufficient?  Also, regarding artifacts and degraded hybridization regions
>> on
>> chips (visible in AffyPLM Residual plots in the form of streaks, blotches,
>> hot spots, etc.),  we are wondering what SCAN.UPC would do with such
>> perturbations?  
>> 
>> 
>> Leif Peterson
>> 
>> HMRI, Houston
> 
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