[BioC] chip area distortion tolerance

[James W. MacDonald]

Thalacker-Mercer, Anna E wrote:
> Hello,
> I have a question in addition to your question about distortions.  How
> much should artifacts influence taking the chip out of the analysis?  I
> have several chips that have decent sized artifacts in them, but seem
> fine when looking at the RLE and NUSE plots.  

If the QA plots look OK, then you can probably use the chips if you are 
using a robust model fit like RMA or GCRMA. Remember that the probesets 
are distributed all over the chip, so an artifact on one section of the 
chip will probably not have a large effect on any one probeset.

Best,

Jim


> 
> Thanks
> Anna
> 
> -----Original Message-----
> From: bioconductor-bounces at stat.math.ethz.ch
> [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of D.Enrique
> ESCOBAR ESPINOZA
> Sent: Monday, December 11, 2006 11:27 AM
> To: bioconductor at stat.math.ethz.ch
> Subject: [BioC] chip area distortion tolerance
> 
> Hi,
> I am doing some QC for chips,
> in the article of HEBER & SICK (2006),
> they use a threshold of 20% of distortion of the area chip.
> 
> !) is there any consensus?
> 2) how do you estimate this %percentage of distortion in R?
> 
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-- 
James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623


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