search for: microbiologi

Dear R users and developers After upgrading to Windows XP and R 1.9.1 and 2.0, I retried to execute plot.baysian() to a data set that I had used previously to plot with no problem in win2000 R1.8. The error I get is: Error in points(Mbar[-index], lods[-index], pch = ".") : only 0's may mix with negative subscripts Thanx in advance Dino P.S. I allready sent this message

Dear R wizards, Hopeful someone can help me with what I believe is a pretty simple task. I pretty new to R so some (much) of the obvious escapes me. How do I get a distance matrix into heatmap? What do I tell distfun if what I'm trying to map is already an ordered distance matrix? I tried >heatmap(x, distfun=as.dist(x)) where x is the distance matrix but R gave me an error. Thanks in

Hi, I am trying to import a tab delimited file (converted from .xls file) by >Test<-read.table("/Users/....txt", header=T, row.names=1) The command has always worked for me, but now I have been getting the error message saying that "duplicate 'row.names' are not allowed. I have checked my original files and all names were unique. I have also tried to change

Hi, I'm trying to build a mixed-effects model in which I'd like to include either a distance matrix or a phylogenetic tree as a random effect. The troubles I've had are that: 1. Function lmer() in package lme4 only accepts a data frame column as a random factor and not a distance matrix. 2. Function MCMCglmm() in package MCMCglmm only accepts a rooted and ultrametric phylogenetic

Dear all, I am a R beginner, and I am looking for a way to do the same thing for all levels of a column in a table. Basically, I have a bunch of protein sequences composed of different amino acid residues, and each residue is represented by an uppercase letter. I want to calculate the ratio of different amino acid residues at each position of the proteins. Here is an example table: Proteins

Can anybody tell me where to find a copy of heatmap2? I've seen it in my travels across the web but didn't bookmark it and can't find it again. Thanks in advance. Paul `-:-. ,-;"`-:-. ,-;"`-:-. ,-;"`-:-. ,-;"`-:-. ,-;"`-:-. `=`,'=/ `=`,'=/ `=`,'=/ `=`,'=/ `=`,'=/ `=` >==/ >==/

Dear friends: I have just read an article entitled " Monitoring of nosocomial invasive aspergillosis and early evidence of an outbreak using cumulative sum tests (CUSUM)", which is published in "Clinical Microbiology and Infection". We have great need to estimate the fluctuation of incidence of IFI in our hospital. But I don't know the details of the stastical method and

OK, so this is a really stupid question and should be incredibly simple to do but I can't figure it out. So maybe someone would be so kind as to tell me. I have a vector of zeros and ones. I want to replace all of the zeros with "black" and all of the ones with "gray". That's it. Any help would be appreciated. Thanks, Paul `-:-. ,-;"`-:-. ,-;"`-:-.

I'm using .C() and .External() and have no problems sending integers, reals or strings from R to C. Nor do I have problems sending integers or reals back from C to R. But I'm pulling my hair out trying to set a string value in a C function and then sending it back from C to to R. I've searched the usual sources and tried various casts, macros and allocation schemes, but I'm

Hi all I am a complete newbie to this list (just subscribed) and a newcomer to R (an S user from olden times). I have been using scatter3d to create a 3d scatter plot with surface. The graphic is created within the rgl package and I have used rgl.postscript to export it so I can generate a publication quality image. My problem is that the plotted surface is no longer transparent in the

Following the "security = domain in Samba 2.x" document in the SWAT documentation page I do this: root@pc194-79:/usr/local/samba/bin# smbpasswd -j MDU -r pv-mdu-server1 -Ujohnm%xxxxxxxx Joined domain MDU. root@pc194-79:/usr/local/samba/bin# This is in [globals]: security = DOMAIN encrypt passwords = Yes password server = pv-mdu-server1 pv-mdu-server2 And now I start Samba via smbd

I'm trying to annotate a density plot and I'm using bquote to paste the sigma symbol next to the numeric text of the standard deviation calculation that I am performing. I have been able to successfully turn the sigma symbol and numeric output the color blue, but when I try to change the font of the text to bold, R doesn't seem to recognize the "font=" command in the same way

OK, I have been wrestling with this for two weeks now, so somebody please help ! We have an existing Samba Print Server, running RedHat linux, kernel 2.2.19, that runs fine, but is a P133 with 64 mb ram. So we built a new PC, the slowest thing we could buy, a duron 1 ghz with 512 mb RAM. Old printer server is running Samba 2.2.5, new printer server is running samba 2.2.5, and Slackware 8.1,

Hi all, I have this microarray large microarray data set (ALL) from which I would like to subset or extract a set of data based on a factor ($mol.biol). I looked up some example of subsetting in, picked up two commands and tried both but I got error messages as follows > testset <- subset(ALL, ALL$mol.biol %in% c("BCR/ABL","ALL1/AF4")) >> Error in

A postdoctoral fellow position in computational biology is anticipated to open in the fall of 2009 at University of Washington, Seattle, WA. The candidate will join a multi-disciplinary group working on edge-cutting research problems in computational biology. Job Description We seek a highly motivated and diligent researcher at the early stage of academic career with the ability to carry out

I have built and uploaded to CRAN the Carbon version of R for MacOS/MacOSX. You'll find the base set (rm151.sit) and the recommended packages (recommended.sit) separately or all in one single file (rm151_FULL.sit) on CRAN and their mirrors soon. I have also built the Bioconductor suite of packages (corresponding to the Bioconductor_1.0.tgz file) as it seems to be one of the most

Dear R gurus and users, for some functions in some of the many packages available for R, with the current definition of \Header given in Rd.sty, the heading bumps into the surrounding words in documentation printed via LaTeX. To alleviate this minor typographical mishap, I'd like to suggest the change to R/doc/manual/Rd.sty included below as a context diff. With this minor diff applied, the

This was ``accidentally'' sent to me rather than R-help ... MM ------- start of forwarded message ------- Thank you very much for your email in downloading the Rgui. I am trying to construct two-line graphs with axis(), but I am lost as to what argument to use to draw the second line. With the xyz.coords, could i use the lty, col... arguments. Please advise me as to what to do with

I have built and uploaded to CRAN the Carbon version of R for MacOS/MacOSX. You'll find the base set (rm151.sit) and the recommended packages (recommended.sit) separately or all in one single file (rm151_FULL.sit) on CRAN and their mirrors soon. I have also built the Bioconductor suite of packages (corresponding to the Bioconductor_1.0.tgz file) as it seems to be one of the most

Dear Sir/Madam, I have tried to install biocoductor package. During the installation, there was an error message showing, there is no XML package available and suggested me to download from the R-project website. Unfortunately I could not find it. Could you give me a hand? Thanks a lot. Cheers, Sen-Lin ------------------------------------------------ Sen-Lin Tang (Ph.D.) Postdoctoral