[BioC] Quality of Affy Chips with the affy package

Rafael A. Irizarry rafa@jhu.edu
Fri, 14 Feb 2003 05:57:24 -0500 (EST)

it's not clear there is a protocol for excluding arrays. as laurent
pointed out, different labs/companies may have different guidelines.  i can
give you two anecdotes of my own:

1- in one specific batch i analyzed i excluded one array (out of 59). a
scatter plot of log intensites with its replicates showed shapes very
different from a straight line with scatter. none of the normalization
procedures fixed it.

2-i had a set of arrays where for some genes i was getting extremely small
within group variances. aftere looking at the histograms i noticed there
was lots of staturation. the genes having this characterisitc happened
to be higly expressed genes. in this particular case i was very careful
when looking at across-condition-to-within-condition ratios of variances
type tests (e.g. t-test, F-test). 

by talking to people who analyze lots of arrays im sure you can learn from
their anecdotes.

hope this helps,

 On Thu, 13 Feb 2003, Oliver Hartmann wrote:

> Dear list members,
> in chapter 4 of "Textual description of affy" several methods for 
> quality control are described: hist(), image(), boxplot() and RNA 
> degradation plots.
> Has anybody used these methods to identify bad quality chips? When do 
> you exclude a chip from further analysis? What's your decision rule?
> Any other suggestions on how to identify bad quality from the data alone?
> Thanks a lot.
> 	-oli-
> -- 
> Oliver Hartmann, Institute of Medical Biometry and Epidemiology
> Philipps-University Marburg, Bunsenstr. 3, D-35037 Marburg
> phone +49(0)6421 28 66514, fax +49(0)6421 28 68921
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