similar to: package pamr: pamr.adaptthresh() error rates

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

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,

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 have binary labels from a nearest shrunken centroids prediction (package pamr). I need to obtain a ROC curve for this test. What is the easiest way to obtain one? Paolo Sonego

Dear List, I am trying to modify the xlab and ylab for a current figure that was plotted by a package, I searched through the low level plotting command and they do not seem to contain how to do this (the only way is to use xlab, ylab as arguments in "plot" command, which I can not do since the plot is plotted using some other package, not by my own script). Is there any command for

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

Dear Stuff, I am trying to enjoy "PAM", but I could not recognize which sample is in which branches in the clustering tree because of too many samples and size limitation for my monitor. I mean, I did unsupervised clustering with "PAM" ( data2$newy<-pamr.makeclasses(data2) ) with 275 primary samples, but samples were piled up at the point of each branch, so I cannot

I am working with microarray analysis and was using PAM with excel interface. Is there a way to do random divisions for the training set in excel? I also tried PAM in R with the pamr menu. How can I do the random divisions in R? Then I tried to reproduce "classification with gene expression data", which is chapter 24 from the book "bioinformatics and computational biology

Dear all, i have microarray data of 3 classes of patients. It's not a time course experiment only steady state. I used a rule-based method to classify the groups by the expression of the genes. This works out so far. Nevertheless I want to check my results with an other method. Therefore I look for one and want to ask you, what you suggest. I have 3 different patient groups, only the steady

Hello, I'm currently using MCRestimate package and I have a question regarding the MCRestimate function. Here is my code: NestedCV.rf<-MCRestimate(eset, "Class", classificatin.fun="RF.wrap", variableSel.fun="varSel.highest.var", poss.parameters= list(var.numbers=c(100), mtry=c(10,50), cross.outer=10,cross.inner=10,cross.repeat=3) I'm pretty sure that I

Greetings! The Bioconductor core group would like to announce the 5th release of Bioconductor, version 1.4. There are many new packages as well as several major upgrades and fixes in older packages, and users are encouraged to upgrade existing tools and check out the new packages. Release 1.4 is intended to be operated with R version 1.9.x, which can be obtained at CRAN

I've started to implement checks for package versions on dependencies in install.packages(). However, this is revealing a number of problems/misconceptions. (A) We do not check versions when loading namespaces, ahd the namespace registry does not contain version information. So that for example (rtracklayer) Depends: R (>= 2.7.0), Biobase, methods, RCurl Imports: XML (>=

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

this is the proposed gssapi diff against OpenSSH-current (non-portable). note: if this goes in, the old krb5 auth (ssh.com compatible) will be removed. please comment. jakob Index: auth.h =================================================================== RCS file: /home/hack/jakob/mycvs/sshgss/auth.h,v retrieving revision 1.1.1.2 retrieving revision 1.3 diff -u -r1.1.1.2 -r1.3 --- auth.h

Dear R-Helpers, I am trying to bootstrap the coefficient of variation on a suite of vectors, here I provide an example using one of the vectors in my study. When I ran this script with the vector x <-c(0.625, 0.071428571, 0.133333333, 0.125, 0), it returned CV(boot) [the second one], and stderr(boot) [the second one] without problem. However, when I ran it with the vector in the

Hi All Please see the Rprofile file which i have modified as follows and after that when I start R then I see that R says to me "TRUE" for all the packages implying that all loaded at once. But when i try to use commands as simple as help("lm"), it doesnt work nor any of the menu "Packages" is not working. Although the regression using lm ( Y ~ X ) is working

Hi, I am running R 2.2.0 on the Windows XP x64. The mechanism of error hanlder seems different. It will take a very long time to pop up a error message diaglog box, even when some simple errors happen such as "Syntax error" or "object xxxx not found". Does anybody have the similar experience? Thanks a lot. BTW: everything works fine under 32-bit Windows XP, error messages