search for: pamr

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():...

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(...

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 pamr.adaptthresh():...

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) mytrain <- pamr.train(mydata) new.scales <- pamr.adaptthresh(mytrain,ntries = 1) ######################################## But if I split the lines i...

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 giv...

...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 doing this? In addition, the package is from CRAN (named Pamr), is there any way that I can modify the function used in the package? Many thanks, Jack [[alternative HTML version deleted]]

...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 monreg muhaz operators pamr Package maintainers whose packages depend on one of these may be natural candidates to become new maintainers. Hence this messages is addressed to all these maintainers via BCC and to R-devel. See <http://CRAN.R-project.org/package=R2HTML> <http://CRAN.R-project.org/package=Semi...

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 hig...

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 recognize them. Can we get the output file with clustered information ? Can we change the size of charactor ? Please let me know how should I do for it. Best regards Nobumoto TOMIOKA...

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

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 d...

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

..., as an alternative is to put the imported package in Depends. The version dependence will in a future release cause an update of XML when rtracklayer is installed, if needed (and available). (B) Things like (package stam) Depends: R (>= 2.7.0), GO.db (>= 2.1.3), Biobase (>= 1.99.5), pamr (>= 1.37.0), cluster (>= 1.11.10), annaffy (>= 1.11.5), methods (>= 2.7.0), utils (>= 2.7.0) are redundant: the versions of method and utils are always the same as that of R. And there is no point in having a package in both Depends: and Imports:, as Biostrings...

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

Art (and group), I'm doing this as a form of missing value analysis. Approximately 30% of the cases are missing data for one variable. To impute values for those cases, I'd like to match those cases that are missing the variable to all other cases and then take an average of those to infill. I realize there are many methods for imputing data. I'm not well versed on any in

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 solutions using R and Bioconductor". There is also an explanation for random divi...

...that it was the "mtry" that led to that warning message. However, I found the information on Bioconductor Code Search:Template.R/MCRestimate/inst/scripts/Template.R, see following: Package: MCRestimate - Version: 2.13.0 - Language: r library(MCRestimate) library(randomForest) library(pamr) library(e1071) the.expression.set <- get(load(DataSet)) if(RF){ list.of.parameter <- c(list(mtry=mtry.range,ntree=ntree.range),parameter.for.preprocessing) r.forest <- MCRestimate(the.expression.set, class.colum, classification.fun=&quo...

...0/13 (total of 33) arrays and the challenge is to classify the groups by the expression of all genes on the hgu133a chip. The named rule-based method found for each group genes, which explain a classification for each sample to one of the groups. Are there packages/method you can suggest? I guess PAMR works not so good for all genes on the chip, right? Would be amazing if you can tell me your opinion. All the best and thanks Peter from the desk of peter kupfer ____________________________________ leibnitz institute of natural product research and infection biology - hans-knoell inst...

...or when mail is an answer to another, extended characters are not well displayed. In some tests we have done, I found more or less the same is happening when using squirrelmail. The funny thing is that the problem dos not appear when using Evolution or Outlook (the MS Office component). I move some pamrs in dovecot.conf and get some results (before moving them, the problem extended to attachements), but still remains as described. Somebody has seen such a behaivour and solved it? I was thinking to change dovecot for another agent, but will be happier using dovecot. Any suggestion? Thanks in advi...

...essing: many improvements, gcrma, affypdnn (probe-dependent nearest neighbors), affyPLM (probe-level models). -- marray (next generation of the depreciated marrayClasses, marrayNorm, marrayPlots, marrayTools packages) -- General analysis tools (rama, qvalue, pickgene, EBarrays, impute, pamr, bim, ) -- QA/QC (arrayMagic, arrayQuality, LPE) -- sequence analysis (pairseqsim, Biostrings) -- interface to the GeneSpring data analysis program (GeneSpring) TOOLS: ====== The released packages include tools which facilitate: * annotation * data management and organization through the u...