Gordon Thanks you so much!!! you are awesome! -Rich On Sun, Jun 26, 2011 at 3:39 PM, Gordon K Smyth <smyth@wehi.edu.au> wrote: > Richard, > > If x is an EList and you want an mdplot of arrays 1 and 3: > > mdplot(x$E[,c(1,3)]) > > Gordon > > ------------------------------**--------------- > Professor Gordon K Smyth, > Bioinformatics Division, > Walter and Eliza Hall Institute of Medical Research, > 1G Royal Parade, Parkville, Vic 3052, Australia. > Tel: (03) 9345 2326, Fax (03) 9347 0852, > smyth@wehi.edu.au > http://www.wehi.edu.au > http://www.statsci.org/smyth > > > On Sun, 26 Jun 2011, Richard Green wrote: > > Wow Gordon, thank you so much. This was extremely helpful. I was able to >> generate some new figures. I couldn't find a lot of info on mdplots() . I >> was able to generate a figure with my whole set of arrays but wasn't able to >> load two individual arrays into mdplots. >> > > My plan was to just have two overlaying MA plots from two different arrays >> in different colors. Any suggestions you have on the simplest way to achieve >> this I would be grateful. Again Thank you Gordon. I really appreciate it! >> > > -Rich >> >> >> >> On Jun 25, 2011, at 6:45 PM, Gordon K Smyth <smyth@wehi.edu.au> wrote: >> >> Hi Richard, >>> >>> The function plotMA() only makes a single plot. As the help page >>> explains, the argument 'array' is an integer rather than a vector. To see a >>> number of plots side by side, you might try mfrow(). For example, to see 2 >>> plots side by side: >>> >>> par(mfrow=c(1,2)) >>> plotMA(x,array=1) >>> plotMA(x,array=2) >>> >>> To see 4 plots: >>> >>> par(mfrow=c(2,2)) >>> plotMA(x,array=1) >>> etc >>> >>> If you have a set of 24 arrays, plotMA() will compare each individual >>> array to the median-array constructed from all the arrays. >>> >>> If you want to compare just two arrays, mdplot() is another convenient >>> alternative. It gives the same results as plotMA() with just two arrays. >>> >>> Best wishes >>> Gordon >>> >>> Date: Fri, 24 Jun 2011 16:01:02 -0700 >>>> From: Richard Green <greener@uw.edu> >>>> To: bioconductor@r-project.org >>>> Subject: [BioC] creating an MA plot with two single channel agilent >>>> arrays >>>> >>>> Howdy, >>>> >>>> I've been generating some individual MA plots but would now like to >>>> generate >>>> an MA plot with two different arrays to compare them. Ideally I'd like >>>> the >>>> two arrays to be different colors so >>>> I can see how they differ >>>> Pasted below is my R session. Any suggestions folks have is appreciated. >>>> -Rich >>>> >>>> library(limma) >>>> >>>> setwd("/vol04/microarray/") >>>> >>>> RG <- >>>> read.maimages(files=dir(),**source="agilent",columns=list(** >>>> G="gMeanSignal",Gb="**gBGMedianSignal",R="**gMeanSignal",Rb="** >>>> gBGMedianSignal")) >>>> >>>> RG <- backgroundCorrect(RG, method="normexp", offset=50) >>>> >>>> RG <- normalizeBetweenArrays(RG$R, method="quantile") >>>> >>>> RG <- log2(RG) >>>> >>>> for (i in 1:24) { >>>> >>>> fname<-paste("/vol04/**microarray/ma_plot",i,".png",**sep="") >>>> >>>> png(fname,300,300) >>>> >>>> print(plotMA(RG, array=i, cex=.2, ylim=c(-1.5,1.5))) >>>> >>>> dev.off() >>>> } >>>> >>>> The above works no problem but when I try to add more than one array I >>>> get >>>> >>>> print(plotMA(RG, array=(1:3,13:16), cex=.2, ylim=c(-1.5,1.5))) >>>>> >>>> Error: unexpected ',' in "print(plotMA(RG, array=(1:3," >>>> >>>>> print(plotMA(RG, array=1:13, cex=.2, ylim=c(-1.5,1.5))) >>>>> >>>> Error in xy.coords(x, y, xlabel, ylabel, log) : >>>> 'x' and 'y' lengths differ >>>> >>> > ______________________________**______________________________**____ ______ > The information in this email is confidential and inte...{{dropped:10}}