[BioC] How to objectively evaluate chip quality?

[Steve Lianoglou]

On Jul 15, 2008, at 1:35 PM, simona dalle carbonare wrote:

> Hi,
> I have a question about quality assessment of microarray chips. Can  
> somebody
> suggest me a quantitative metric to evaluate the chips and in  
> particular the
> plot about the quality of the chip (for example boxplot of intensity)?


"Quality control through Data Exploration" section of the `affy`  
vignette in the `affy` library:
http://bioconductor.org/packages/2.2/bioc/vignettes/affy/inst/doc/affy.pdf

and the `QualityAsses` vignette in the `affyPLM` library:
http://bioconductor.org/packages/2.2/bioc/vignettes/affyPLM/inst/doc/QualityAssess.pdf

address QA issues a bit and include several visualizations. Is that  
what you had in mind?

-steve

--
Steve Lianoglou
Graduate Student: Physiology, Biophysics and Systems Biology
Weill Cornell Medical College

http://cbio.mskcc.org/~lianos