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

[Jordi Altirriba Gutiérrez]

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