[BioC] how to make an MA plot with single color agilent microarray?

[Wolfgang Huber]

Hi Richard

Il Jun/19/11 4:19 AM, Richard Green ha scritto:
> Could someone suggest the best way to create an MA plot from 14 single color
> agilent arrays? I would really appreciate it. Thanks -Rich
>

One option is to compute a virtual mean (or median) reference array and 
to make 14 MA-plots of each array against that reference. Essentially, 
you redefine the 'A' to be the average of all arrays rather than just of 
a pair, and then compute 14 different 'M's.

The MA plot is just an orthogonal transformation of the ordinary 2D 
scatterplot. In that sense, any other linear transformation of your 
14-dimensional dataset could also be useful (e.g. PCA), in particular if 
one of the new axes aligns with the (1,1,1,..,1) direction.

(A variant of the 'virtual reference array' idea is used in the MA plots 
in the reports generated by 'arrayQualityMetrics', which you can see by 
running the R script associated with the vignette
http://www.bioconductor.org/packages/devel/bioc/html/arrayQualityMetrics.html 
  -> "Introduction: microarray quality assessment with arrayQualityMetrics")

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