[BioC] quality assessment of microarray using arrayQualityMetrics

[Wolfgang Huber]

Dear Amit

have a look at the manual page of the 'arrayQualityMetrics' function. 
There, you can see that it accepts 'MAList' objects directly, and 
extracts the needed information from that.

Another way to learn more about this package is its vignette, which you 
can view with
  vignette("arrayQualityMetrics")

	Best wishes
	Wolfgang


> Dear All,
> 
> I am working on large dataset of two color arrays. For two color
> arrays the normalizeBetweenArray function (limma) produces MAList from
> RGList after normalization. My question is after normalization of two
> color microarray data, whether arrayQualityMetrics should be run on M
> (log ratios) matrix or A (average log intensity) matrix ? I am
> guessing it should be run on A matrix as arrayQualityMetrics requires
> matrix of microarray intensities to perform the analysis. But, I am
> not sure. Any suggestion is appreciated.
> 
> regards
> Amit
> 
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-- 


Wolfgang Huber
EMBL
http://www.embl.de/research/units/genome_biology/huber