[BioC] Re: how to evaluate the arrays quality?

[Crispin Miller]

Hi,
You may also want to have a look at this:

http://bioinf.picr.man.ac.uk/simpleaffy/qcstats.jsp

Cheers,
Crispin
 

-----Original Message-----
From: bioconductor-bounces at stat.math.ethz.ch [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Jordi Altirriba Gutiérrez
Sent: 03 June 2005 15:59
To: hanweinong at yahoo.com; bioconductor at stat.math.ethz.ch
Subject: [BioC] Re: how to evaluate the arrays quality?

Dear Han,

>before starting any analysis on Affymetrix arrays is important to 
>evaluate the arrays quality.
>How to evaluate the Affymetrix Genechips  image artifacts is ok, ugly 
>or bad but still reasnable >using  using the fitPLM of the affyPLM package?

>How to write the scripts?

About the package affyPLM, I would recomend:
1.- Read the vignette:
affyPLM: Model Based QC Assessment of Affymetrix GeneChips
2.- Go to the Ben Bolstad web page, where you can see useful images of artifacts and "bad" chips:
http://www.stat.berkeley.edu/~bolstad/PLMImageGallery/

About the arrays quality, I would recommend to do some quality controls of the Affy package (boxplots, histograms, images of the chip, RNA degradation plots, etc.)

HTH

Jordi Altirriba

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