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Hi all, I've got a set of gene expression data, and I'm plotting several heatmaps for subsets of the whole set. I'd like the heatmaps to have the same color distribution, so that comparisons may be made (roughly) across heatmaps; this would require that the color distribution and distance functions be based on the entire dataset, rather than on individual subsets. Does

I'm working on some heatmaps, and the person I'm working with would prefer a red-black-green color palette (red denoting gene induction and green denoting gene repression). Does such a palette exist already? If not, is there an easy way to create one? Thanks, Jake

Hi all, I'm trying to build R 2.1.1 on Ubuntu 5.04 i686-SMP. Configure goes well with: ./configure --with-BLAS --with-readline=no but once I run 'make', I get the following error: In file included from devX11.c:64: devX11.h:57:74: X11/Intrinsic.h: No such file or directory Any ideas? Thanks in advance, Jake

Hi all, In heatmap's documentation, it mentions that the output value is actually an invisible list...how would one access this list? Thanks, Jake

Does anyone know how to extract residuals in lmer? Here's the error I get: > crop.lme=lmer(response~variety*irrigation*pesticide+(1|rep)+(1|rep: pesticide)+(1|rep:pesticide:irrigation), crop.data) > qqnorm(crop.lme) Error in qqnorm.default(crop.lme) : y is empty or has only NAs > resid(crop.lme) NULL Thanks! --Jake

Hi all, Does anyone know of a fairly easy way to "stretch" a heatmap vertically? I've got 42 arrays and would like to be able to see as many significant genes as possible (right now I can only get 50 genes with it still being readable). In some comparisons there are several hundred significant genes. I've fiddled with the "asp" argument, but that doesn't

I did a very quick search of the archive and couldn't find a readily available answer to this one: I'd like to convert, for example: c("a", "b", "a", "b") to c(1, -1, 1, -1) In the case of the first vector, it may be any length, but will always only have two unique values. It must always be replaced by corresponding values of 1 and -1. Any

Hi all, I would like to be able to call a custom function automatically before plot.new() is called (more specifically, before a new plot is created on the current graphics device). Recently I've been poking around in the help files of some of the low(er) level plotting functions, and I seem to remember something saying that you could somehow add a setting to call a function immediately

Hi all, I've been using R for a while, but was puzzled when I just barely noticed this behavior: > x <- 1:10 > names(x) <- c("a","b","a",letters[1:7]) > x a b a a b c d e f g 1 2 3 4 5 6 7 8 9 10 > x["a"] a 1 ... that is, if a vector has identical (and therefore ambiguous) names, it only returns the first

Hi All, I'm taking an Experimental Design course this semester, and have spent many long hours trying to coax the professor's SAS examples into something that will work in R (I'd prefer that the things I learn not be tied to a license). It's been a long semester in that regard. One thing that has really frustrated me is that lme has an extremely counterintuitive way for

---------- Forwarded Message ---------- Subject: Re: [R] conditional coloring of image labels Date: Friday 11 November 2005 1:04 pm From: jim holtman <jholtman at gmail.com> To: Jake Michaelson <jjmichael at cc.usu.edu> Use 'mtext': genes=cbind(ABC1=c(3,4,4,5,6,3), ABC2=c(4,3,4,7,7,8), ABC3=c(8,7,8,6,3,2)) ###plot the image image(1:nrow(genes), 1:ncol(genes), genes, axes =

Hi all, I am interested in plotting a heatmap of a set of genes. I would like the text labels of these genes to be colored red rather than black if they meet certain statistical criteria (using an if statement). I'm not sure how to change individual color labels without changing them all. Can anyone provide some insight on how to do this? Thanks in advance, Jake

Is there a way to specify the color of the main title, the subtitle, or the axis labels? I mean, for instance, something like title(main="cougar", col=2) For me, the above command produces the color black; that is, the "col" argument has no effect. I'm on a Windows 2000 machine with > version _ platform i386-pc-mingw32 arch i386 os mingw32 system

Is there any documentation on what kind of SPSS file can and cannot be read by read.spss? Alternatively, how can one modify or "clean" an SPSS file to make it readable by read.spss? What properties must a *.sav file before read.spss can read it? The file in this example is 270KB, with 5 rows and 173 columns. I have no trouble reading larger files with read.spss, so it's not

Is there a way to force the puppetmaster to resign certificates for existing certificates when a new CSR for the same hostname arrives? When we reinstall freshly formatted clients with puppet (with the same hostname) the puppet client complains: err: Could not request certificate: Retrieved certificate does not match private key; please remove certificate from server and regenerate it

Hi all, I've got some image plots on which I'd like to include some gene information (in the margins using mtext). Unfortunately, the description is rather long and will need to be wrapped to fit on several lines. From what I know about mtext, it's really only meant for single-line labels, not paragraphs. Here's some sample code of the idea I'm trying to accomplish:

Suppose we have some glm object such as: myglm <- glm( y ~ x, data=DAT) Is there an elegant way--or the "right way" within the R way of thinking--to obtain the names of the response variable, the predictor variables, and the dataset, as character strings? For instance, suppose the "right way" was to use the (currently fictitious) functions theresponse(), thepredictors(),

How would I create the following plot using lattice? symbols( combPsummary$pastRate, combPsummary$finRate, circles=sqrt(combPsummary$N) ) The idea is to plot finRate vs pastRate using circles whose areas are proportional to the number of people in each group. The following attempt does not really work: xyplot( finRate ~ pastRate , data=combPsummary , panel=function( x, y,

I'm having the exact problem outlined in a previous post from 2005 - unfortunately the post was never answered: http://tolstoy.newcastle.edu.au/R/help/05/10/15055.html When running: lm2=lars(x2,y,type="lasso",use.Gram=F) I get an error: Error in if (zmin < gamhat) { : missing value where TRUE/FALSE needed ...when running lasso via lars() on a 67x3795 set of predictors. I

help.search("groupedData") says that it's part of the lme4 package, but it appears not to be there (details below). Is this because lme4 is new and (perhaps) still under development? > update.packages() trying URL `http://cran.r-project.org/bin/windows/contrib/1.9/PACKAGES' Content type `text/plain; charset=iso-8859-1' length 19113 bytes opened URL downloaded 18Kb >