similar to: Fwd: Re: conditional coloring of image labels

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

Hi, maybe someone can help me with this: I have a matrix of genes and values: GeneName Value Abc1 10 Abc2 11 Bbc1 -5 Bbc31 2 Ccd 5 Ccd -2 Ccd 7 Dda 5 Dda 10 ..... ..... Zzz3 -1 I would like to

Hi, I'm new to R (and statistics) and my boss has thrown me in the deep-end with the following task: We want to evaluate the impact that sampling size has on our ability to create a robust model, or evaluate how robust the model is to sample size for the purpose of cross-validation i.e. in our current project we have collected a series of independent data at 250 locations, from which

Hi, how can I change a defined factor-variable? Like adding levels, renaming existing levels or merge several levels of a factor to one level? For example; following factor-variable is given: x <- factor(c("xyz1", "abc1", "xyz2", "abc2")) How can I add the level fgh? And how can I merge "xyz1" and "xyz2" to one level? And

Hi together, after I read "very often" without even a tiny bit of a contradiction, I start to have the feeling I have a basic misunderstanding of rsync. Assume one want to get a list of files which would have been transfered by rsync if rsync was requested to sync directories X and Y and one does <code> X=`mktemp` echo "abc" > $X/1 echo "abc1" > $X/2

Wayne, While testing rsync 2.6.8, I often receive broken pipe error, even though there is no network problem, between Active and Standby nodes. Please clarify. 2007/01/09 02:11:36 [1076] rsync: connection unexpectedly closed (342821 bytes received so far) [receiver] 2007/01/09 02:11:36 [1076] rsync: writefd_unbuffered failed to write 84 bytes [generator]: Broken pipe (32) 2007/01/09

We are seeking a talented and driven postdoctoral fellow to join the laboratory of Jake Michaelson, PhD, assistant professor in the department of psychiatry at the University of Iowa. The Michaelson lab investigates the effect of genetic variation on the development and function of the brain, particularly in the context of neurodevelopmental conditions such as autism and language impairment. Our

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 Others can have better insight in your question so i tis preferable to post your mails to the Rhelp list too. I hope your datafile is all numeric. If not after t(datafile) can be character. AFAIK your pvalue is not propagated to aov function. Based on artificial data your construction arrives to result, which in this case tells you that there is almost no difference in those 5 groups.. m

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

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

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, My data genes [,1] [,2] [,3] [,4] [1,] 25 72 23 55 [2,] 34 53 41 33 [3,] 26 43 26 44 [4,] 36 64 64 22 [5,] 47 72 67 34 stu<-t.test(genes[,1:2],genes[,3:4]) > stu$p.value [1] 0.4198002 i get 1 pvalue for the entire col1:col2 Vs col3:col4. I am trying to get 5 p values for the 5 rows i have. I am trying to avoid a for loop coz my

Does anyone have code that will methodically process R sourcecode, turning T's into TRUE and F's into FALSE? I got bored doing this by hand, after the first 30-odd functions-- there are hundreds left to do. I don't want to simply deparse everything, because that would destroy my beautiful formatting. The reason it's not trivial, is that comment lines, quotes, and split lines need

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

Hi! All, To find co-expressed genes from a expression matrix of dimension (9275 X 569), I used rcorr function from library(Hmisc) to calculate pearson correlation coefficient (PCC) and their corresponding p-values. From the correlation matrix (9275 X 9275) and pvalue matrix (9275 X 9275) obtained using rcorr function, I wanted to select those pairs whose PCC's are above 0.8 cut-off and then

Hi, I used GOstats to perform enrichment test on a set of genes (20). There are 7 GO terms with pvalue less than cuttoff and therefore shown in the result table. How can I get the information that which gene in the input gene set belong to which GO term of these enriched GO terms? Thanks for any comments. best, Tim [[alternative HTML version deleted]]

I've been using R for a while under Mac OS X, which thanks to the R on OS X developers, is probably the best platform for learning R. I recently built a Linux box with a Pentium D processor, and am running an AMD64 port of Ubuntu with the SMP kernel. After setting up the basics on the box, I thought I'd install R as well. I've had a very hard time finding good documentation

I've been using R for a while under Mac OS X, which thanks to the R on OS X developers, is probably the best platform for learning R. I recently built a Linux box with a Pentium D processor, and am running an AMD64 port of Ubuntu with the SMP kernel. After setting up the basics on the box, I thought I'd install R as well. I've had a very hard time finding good documentation

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