similar to: replace non numeric with "NA"

Hi,   I need to generate a heatmap on a square matrix and wouldn't want to reorder the columns and the rows on the heatmap display.    I have used the options Rowv=NULL and Colv=NULL but doesn't seem to work. Following is a snippet of the heatmap function i am using. args <- commandArgs(); inputfile <- args[2] imgfile   <- args[3] bitmap(imgfile, height=15, width=15, res=100,

Hello , I am trying to create a histogram in order to compare between two groups and would like it to be similar to the figure attached. How can I generate this using R ? Thank you, Nandini http://r.789695.n4.nabble.com/file/n3582448/5634-15977-1-PB.gif -- View this message in context: http://r.789695.n4.nabble.com/Histogram-tp3582448p3582448.html Sent from the R help mailing list archive at

Can biomaRt connect to data base "http://mirecords.umn.edu" or a branch of it ... for instance the validated miRNAs list ..? Thank you very much. Maura tutti i telefonini TIM! [[alternative HTML version deleted]]

Hi, I am using R 2.8.1 version on Windows with RGui. I have loaded pls package lattest version (2.1-0). When I try to load this package in R using library(pls) command, the following error message appear: Erreur dans library(pls) : 'pls' n'est pas un package valide -- a-t-il ?t? install? < 2.0.0 ? Could you please help me to solve this problem? Regards Damien -- View this

I can't seem to find info on how to unload packages that have been loaded. My goal in doing so is to gain access to functions that have been masked out by those packages. Or is there another way to do so? Thanks in advance. Jim Bouldin, PhD Research Ecologist Department of Plant Sciences, UC Davis Davis CA, 95616 530-554-1740

hello if there is a package can do blast in R? [[alternative HTML version deleted]]

Hi, I am analysing gene expression data using the heatmap.2 function in R and I was wondering what is the formula of the "raw z-score" bar which shows the colors for each pixel. According to that post: https://mailman.stat.ethz.ch/pipermail/r-help/2006-September/113598.html, it is the (actual value - mean of the group) / standard deviation. But, mean of which group? Mean of the gene

Hi all, I'm just tried to start analysing some micro-array chips. And R was asking for this package. When I tried to install it it says that: Using R version 2.10.1, biocinstall version 2.5.10. Installing Bioconductor version 2.5 packages: [1] "hugene10stv1cdf" Please wait... Warning message: In getDependencies(pkgs, dependencies, available, lib) : package ?hugene10stv1cdf? is

I am running a simple SQL SELECT statement that involvs 50k + data points using R and the RJDBC interface. I am facing very slow response times in both the RGUI and the R console. When running this SQL statement directly in a SQL client I have processing times that are a lot lot faster (which means that the SQL statement itself is not the problem). Did any of you compare RJDBC vs RMySQL or is

Hi, I'm using Sweave to prepare a descriptive report. Are at least 20 tables built with xtable command of kind: <<echo=F, results=hide>>= q5 = factor(Q5, label=c("N?o", "Sim")) (q5.tab = cbind(table(q5))) @ <<echo=F, results=tex>>= xtable(q5.tab, align="l|c", caption.placement = "top", table.placement='H') @ I'm

I would like to build a package for the HT HG-U133+ PM arrays from affy, but I can't find any good documentation on how to go about it. Naively using makecdfenv's make.cdf.package() causes R to seg-fault. I'm unfamiliar with the CDF format as such, but I'm guessing that it's changed somewhat because the PM arrays no longer have P/A and mismatches. I'm looking to build

Hi, I am trying to run affylmGUI on my mac computer. I have already installed the Tlc package as well as Bwidgets through ActiveTcl conversion installing files. However, when running affylmGUI() on R, I keep getting the message in the attached file. I have copied the tcl folders from the root library to the user library, and have obtained the same issue. I would really appreciate if

Hello dear R help group, I would like to download the tRNA data on: http://gtrnadb.ucsc.edu/download.html And then import it into R. Can anyone direct me as to how to do so? Thanks, Tal ---------------------------------------------- My contact information: Tal Galili E-mail: Tal.Galili@gmail.com Phone number: 972-52-7275845 FaceBook: Tal Galili My Blogs: http://www.talgalili.com (Web and

Hello, I am trying to calculate the median of numbers across each row for the data shown below , with the condition that if the number is negative, that it should be ignored and the median should be taken of only the positive numbers. For eg: data is in Column A,B,C. Column D and E demonstrates what I want to get as answer A B C Median median value -13.6688115 -32.50914055

Hi folks, I created a subset of a dataframe (i.e., selected only men): subdata <- subset(data,data$gender==1) After a residual diagnostic of a regression analysis, I detected three outliers: linmod <- lm(y ~ x, data=subdata) plot(linmod) Say, the cases 11,22, and 33 were outliers. Here comes the problem: When I want to exclude these three cases in a further regression analysis, - for

Hi all, In the package rtlu, I use the function savePlot. It is convenient since it let the user decide in which graphic format he wants his graph to be export. But when I run R CMD check, I get the following message : > rtlu(V1,fileOutput="First.tex",textBefore="\\section{Variable 1 to 3}",graphName="V1") Error in savePlot(filename = nomBarplot, type = type)

Hello R Folks... Not a technical question, but I need some advice and perspective. I?ve got a set of functions I?m planning to put together into a package. The main hunk of data that gets used by different functions is currently an S3 list. I?ve been reading about S4 objects, and I see the (numerous) advantages of them. I have seen the recommendation that all new packages be done with S4.

Dear all, I am using R version 2.9.2 in Windows. I would like to output the results of a function I have written to a .txt file. I know that I can do this by using the code write.table(boothd(10),"boothd10.txt",sep="\t",append=TRUE) etc. However, I would like to bootstrap my function 'boothd' several times and get each vector of results as a new line in my text

I've been trying to figure out how to read in a large file for a few days now, and after extensive research I'm still not sure what to do. I have a large comma delimited text file that contains 59 fields in each record. There is also a header every 121 records This function works well for smallish records getcsv=function(fname){ ff=file(description = fname) x <- readLines(ff)

Hello, I am trying to extract a subset of a dataframe A (2 columns) by extracting all entries in A (several repeated entries) that match dataframe B in both columns. For example, part of A and B are shown below. The following does not seem to work correctly. This only seems to select on the first component and all instances of the second. ind <- A$C1 %in% B[,1] & A$C2 %in% B[,2]