[BioC] Plate or print-order effects - limma

Tue Jan 2 21:38:52 CET 2007

Hi Gordon,

FYI - I was playing around with plotting print order effects, and found a 
discrepancy between the help documentation and the actual behavior of 
'normalizeForPrintorder.rg '. The help file states "The function 
plotPrintorder or normalizeForPrintorder.rg with plot=TRUE returns no value 
but produces a plot as a side-effect." However, when I used 
'normalizeForPrintorder.rg' with plot=TRUE, it not only produced the plot 
but spit out the entire list!

I'm using this function instead of the wrapper 'plotPrintorder' because I'm 
having trouble making the necessary layout list. I could only find a little 
bit of information about the layout list in 'printorder' help page - is 
each component of the list (ngrid.r, ngrid.c, nspot.r and nspot.c) just a 
single number? In my case our printer has 48 tips and prints 12 x 4 blocks 
of 420 spots, one dip per spot, so would my layout just be a list of 
ngrid.r = 12, ngrid.c = 4, nspot.r = 420, and nspot.c = 1?

Thanks,
Jenny

 > sessionInfo()
R version 2.4.0 (2006-10-03)
i386-pc-mingw32

locale:
LC_COLLATE=English_United States.1252;LC_CTYPE=English_United 
States.1252;LC_MONETARY=English_United 
States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252

attached base packages:
[1] "splines"   "tools"     "methods"   "stats"     "graphics"  "grDevices"
[7] "utils"     "datasets"  "base"

other attached packages:
  affyQCReport    simpleaffy         made4 scatterplot3d          ade4
      "1.12.0"       "2.8.0"       "1.8.0"      "0.3-24"       "1.4-2"
       affyPLM      affydata affycoretools       annaffy        xtable
      "1.10.0"      "1.10.0"       "1.7.5"       "1.6.0"       "1.4-2"
         gcrma   matchprobes       biomaRt         RCurl           XML
       "2.6.0"       "1.6.0"       "1.8.0"       "0.7-0"       "1.2-0"
       GOstats      Category    genefilter      survival          KEGG
       "2.0.3"       "2.0.3"      "1.12.0"        "2.29"      "1.14.1"
          RBGL      annotate            GO         graph         limma
      "1.10.0"      "1.12.0"      "1.14.1"      "1.12.0"       "2.9.1"
          affy        affyio       Biobase       RWinEdt
      "1.12.1"       "1.2.0"      "1.12.2"       "1.7-5"

At 09:32 PM 12/31/2006, Gordon Smyth wrote:
>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/>
> > > ________________________________
> > >
> > > 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
>
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Jenny Drnevich, Ph.D.

Functional Genomics Bioinformatics Specialist
W.M. Keck Center for Comparative and Functional Genomics
Roy J. Carver Biotechnology Center
University of Illinois, Urbana-Champaign

330 ERML
1201 W. Gregory Dr.
Urbana, IL 61801
USA

ph: 217-244-7355
fax: 217-265-5066
e-mail: drnevich at uiuc.edu