similar to: SVM? Comparison method wanted: 3 Groups, Microarray data

Hello R Users, I am a new user to R. When we make a simple plot then how to increase the font size of the data at the each axis. Many thanks, Kind regards, Yogesh -- =========================================== Yogesh Tiwari, Max-Planck Institute for Biogeochemistry, Hans-Knoell Strasse 10, D-07745 Jena, Germany Office : 0049 3641 576 376 Home : 0049 3641 223 163 Fax : 0049 3641

Hallo, I just installed all needed packages for my project on my PC. But I cannot load all at one time. I now want to load limma. How can I realize the following plan: I want to install for example limma inclusive all needed other sub packages (add-on). Can anyone tell me the corresponding command? Thanks, Corinna Here is the result of the command library(): Pakete in Library

Hello, When I plot any data with simple plot command in R, for example :- plot(time,co2,ylim=c(350,380),xlim=c(1993,2003),xlab=NA,ylab=NA,type="p",col=5) Then the first value of x-axis(350) and y-axis(1993) never starts from origin, always they sifted from the origin. Is there any command that I can correct this in the ploted figure and both the axis values start from origin.

Hello, I have red the E-mail from Christophe Dumont from 17 Mar 1997We have a similar problem. In our smb.conf we have the entries: [global] hosts allow = 193.174.234., 192.124.248., 193.174.235., 141.35.191.122 workgroup = IMBNET printing = SYSV printcap name = /etc/printcap load printers = yes passwd program = /usr/bin/yppasswd share modes = yes browseable = yes ....

Hello 'R' Users, I am very new on 'R', so excuse me if I ask something wrong. I have ASCII data and the colums of the data are looks like :- !------------------------- time,yr,mo,dy,hr,min,sec,lat,lon,ht,co2obs,sigma,co2model -- - -- !---------------------------- Each column has data value. Now I want to produce 2-d color maps, for example the plot should look like :- on

Hi, I was working on a classification problem using the pamr package. I used the pamr.adaptthresh() function to find the optimal accuracy of the classifier. I must not be doing it right, since it doesn't return the threshold values for optimum classification. For example,if I run it on a dataset, I get the following result using pamr.adaptthresh(): predicted true

Hi, I was working on a classification problem using the pamr package. I used the pamr.adaptthresh() function to find the optimal accuracy of the classifier. I must not be doing it right, since it doesn't return the threshold values for optimum classification. For example,if I run it on a dataset, I get the following result using pamr.adaptthresh(): predicted true (1)

Hi, Sorry about the earlier formatting errors... I was working on a classification problem using the pamr package. I used the pamr.adaptthresh() function to find the optimal accuracy of the classifier. I must not be doing it right, since it doesn't return the threshold values for optimum classification. For example,if I run it on a dataset, I get the following result using

Hi, I must be missing something here...Essentially, a short piece of code works if it's standalone, but doesn't work if it's divided into two functions. The code that works is: ################### WORKS ############### library(pamr) set.seed(120) x <- matrix(rnorm(1000*20),ncol=20) y <- sample(c(1:4),size=20,replace=TRUE) mydata <- list(x=x,y=y)

Hi, I have tried some time trying to figure out how to use pamr to plot multiclass Estimated probabilities for the training data and test data? Specifically, how to recreate the PAMR publication on PNAS with Tibshrani et al. The publication is as attached. The plot I want to do is Figure 5. I have downloaded the pamr package and the function which gives similar plot is pamr.plotcvprob

Hello, Im trying to combine 3 affybatches (1x hgu133+2 array and 2x hgu133a array) Im useing this script: library(matchprobes) library(affy) library(AnnotationDbi) library(hgu133plus2probe) library(hgu133aprobe) library(hgu133a.db) u133p2 = ReadAffy() # reading hgu133 +2 cel file into affybatch u133a1 = ReadAffy() # reading hgu133a cel file into affybatch u133a2 = ReadAffy() # reading hgu133a

On Mon, Jan 26, 2015 at 12:24 PM, Hadley Wickham <h.wickham at gmail.com> wrote: > If it was any other environment than the global, you could use substitute: > > e <- new.env() > delayedAssign("foo", stop("Hey!"), assign.env = e) > substitute(foo, e) > > delayedAssign("foo", stop("Hey!")) > substitute(foo) Hmm... interesting

1. According to the doc of PAMR, the shrinkage threshold is determined by cross-validation. Does this mean that user need not tune any parameter? 2. I tried two applications using PAMR, the results are very disappointing. The attached are the cross-validation results. You can see that the classification errors are relatively high (0.2 at the best), in the case of two categories classification,

Hi, I got an interesting programming challenge: How do you inspect an object which is assigned via delayedAssign() and that throws an error as soon as it is "touched" (=the value is evaluated)? Is it possible? MINIMAL EXAMPLE: $ R --vanilla > delayedAssign("foo", stop("Hey!")) (If you find this minimal example silly/obvious, please skip down to the real

If it was any other environment than the global, you could use substitute: e <- new.env() delayedAssign("foo", stop("Hey!"), assign.env = e) substitute(foo, e) delayedAssign("foo", stop("Hey!")) substitute(foo) Hadley On Mon, Jan 26, 2015 at 12:53 PM, Henrik Bengtsson <hb at biostat.ucsf.edu> wrote: > Hi, I got an interesting programming

Dear maintainers and R-devel, Several orphaned CRAN packages are about to be archived due to outstanding QC problems, but have CRAN and BioC packages depending on them which would be broken by the archival (and hence need archiving alongside). Therefore we are looking for new maintainers taking over maintainership for one or more of the following packages: R2HTML SemiPar cghseg hexbin lgtdl

Hello, I am writing an interface to some functions from the CRAN package pamr, which is poorly written. I have a S4 method I declared with setMethod. I'd like to provide a signature of "pamrtrained" which is the class of object that training creates. The last two lines of code of pamr.train are : class(junk) = "pamrtrained" junk How can I dispatch on these kinds

Hello, I want to use expresso for preprocessing the hgu133a-spikein data from affycompII. But there is an error: > library(affy) > path <- "z:/Microarray/hgu133a-spikein/rawdata" > celFile <- list.celfiles(path=path,full.names=TRUE); > affyBatch <- ReadAffy(filenames=celFile[1:6]); > eset1 <-

Dear all, i searched for some classification methods and I have no glue if i took the right once. My problem: I have a matrix with 17000 rows and 33 colums (genes and patients). The patients are grouped into 3 diseases. No I want to classify the patients and for sure i want to know which rows are more helpful for the classification than others. I tried SVM and random forest. Do you think this

Hi, I am wondering how to make a function Fun to make the following work: t0 <- (paste("hgu133a", "ENTREZID", sep="")) xx <- as.list(Fun(t0)) # make it work like xx<-as.list(hgu133aENTREZID) thanks, -- Weiwei Shi, Ph.D Research Scientist GeneGO, Inc. "Did you always know?" "No, I did not. But I believed..." ---Matrix III