[BioC] Plate or print-order effects - limma

hdvi at well.ox.ac.uk hdvi at well.ox.ac.uk
Tue Jan 2 22:07:59 CET 2007


Dear Jenny

As I recall, ngrid.r & ngrid.c are the number of grid rows and columns, so
12 and 4 in your case, while nspot.r & nspot.c are the number of spot rows
and columns within each grid block, probably 20 and 21 for you. I don't
think the number of dips per spot is taken into account.

HTH
\Heidi

> ...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
>
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