[BioC] how to make an MA plot with single color agilent microarray?
whuber at embl.de
Sun Jun 19 09:43:04 CEST 2011
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
-> "Introduction: microarray quality assessment with arrayQualityMetrics")
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