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

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 > >_______________________________________________ >Bioconductor mailing list >Bioconductor at stat.math.ethz.ch >https://stat.ethz.ch/mailman/listinfo/bioconductor >Search the archives: >http://news.gmane.org/gmane.science.biology.informatics.conductor 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

Dear Gordon Smyth, Thanks for the information. Concerning the analysis of variance that you did in http://www.statsci.org/smyth/pubs/porder/porder.html, I would like to know how did you made the table in that format, with between and within genes? Kind regards, Jo?o Fadista -----Original Message----- From: Gordon Smyth [mailto:smyth@wehi.EDU.AU] Sent: Monday, January 01, 2007 4:32 AM To: J.delasHeras at ed.ac.uk; Jo?o Fadista Cc: bioconductor at stat.math.ethz.ch Subject: [BioC] Plate or print-order effects - limma 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