[BioC] Plate or print-order effects - limma

[Gordon Smyth]

Dear Joao,

See ?plotPrintorder and 
http://www.statsci.org/smyth/pubs/porder/porder.html. (I'm a bit 
puzzled why you haven't already tried this, considering that you're 
already using limma and are aware of printorder effects.)

Note that GAL file order is not the same as printorder in general, so 
you can't just use plot().

Best wishes
Gordon

>Date: Fri, 22 Dec 2006 19:33:11 +0000
>From: J.delasHeras at ed.ac.uk
>Subject: Re: [BioC] Plate or print-order effects - limma
>To: bioconductor at stat.math.ethz.ch
>
>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/>
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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
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