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.
Jose
Quoting Jo?o 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
>
> Jo?o Fadista
> Ph.d. student
>
>
>
> Danish Institute of Agricultural Sciences
> Research Centre Foulum
> Dept. of Genetics and Biotechnology
> Blichers All? 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=""/>
> ________________________________
>
> News and news media
<http: www.agrsci.org="" navigation="" nyheder_og_presse=""> .
>
> This email may contain information that is confidential. Any use or
> publication of this email without written permission from DIAS is
> not allowed. If you are not the intended recipient, please notify
> DIAS immediately and delete this email.
>
>
> [[alternative HTML version deleted]]
>
>
--
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
Swann Building, Mayfield Road
University of Edinburgh
Edinburgh EH9 3JR
UK
