[BioC] Plate or print-order effects - limma

J.delasHeras at ed.ac.uk J.delasHeras at ed.ac.uk
Fri Dec 22 20:33:11 CET 2006

Just use 'plot':

is MA is teh name of your MAlist containing your M and A values, then

plot(MA$A[,1],MA$M[,1]) #prints the usual MA plot for slide 1

plot(MA$M[,1]) #prints the M values, in the order given in the gal  
file (by block)... is that what you wanted?

just add your favourite parameters to 'plot' to make it look the way  
you want it.


Quoting João Fadista <Joao.Fadista at agrsci.dk>:

> Dear all,
> I would like to visualize, for each array, the plate or print-order   
> effects. To do that I want to be able to plot the M values in the   
> vertical axis and the print order (i.e., the numerical order in   
> which the spots were laid down during the printing of the array) in   
> the horizontal axis. I am using genepix files.
> Thanks in advance,
> Best regards
> João Fadista
> Ph.d. student
>  	 Danish Institute of Agricultural Sciences
> Research Centre Foulum
> Dept. of Genetics and Biotechnology
> Blichers Allé 20, P.O. BOX 50
> DK-8830 Tjele
> Phone:	 +45 8999 1900
> Direct:	 +45 8999 8999
> E-mail:	 Joao.Fadista at agrsci.dk <mailto:Joao.Fadista at agrsci.dk>
> Web:	 www.agrsci.org <http://www.agrsci.org/>
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Dr. Jose I. de las Heras                      Email: J.delasHeras at ed.ac.uk
The Wellcome Trust Centre for Cell Biology    Phone: +44 (0)131 6513374
Institute for Cell & Molecular Biology        Fax:   +44 (0)131 6507360
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