search for: pnas

Hi all, In Tibshirani's PNAS paper about nearest shrunken centroid analysis of microarrays (PNAS vol 99:6567), they used cross validation to choose the amount of shrinkage used in the model, and then test the performance of the model with the cross-validated shrinkage in separate independent testing set. If I don't have th...

Dear friends - a couple of papers in PNAS (lastly:framework for making better predictions by directly estimating variables' predictivity, Lo et al PNAS 2016; 113:14277-14282) have focused interest on mapping complex traits to multiple loci spread all over the genome. I have been around on the relevant taskview(s) I hope but fail to...

Q: Has anyone implemented cartograms [**] in R? A search on the R site turned up https://stat.ethz.ch/pipermail/r-sig-geo/2005-December/000698.html which led to http://www.okada.jp.org/RWiki/index.php?cmd=read&page=Rmap%A4%F2%BB% C8%A4%C3%A4%BF%C3%CF%BF%DE%C9%BD%BC%A8&word=Rmap#content_1_35 which has (one form of) a cartogram as a PNG, but which doesn't seem to have code. (The

Dear List, We are planning a genotyping study to be analyzed using false discovery rates (FDRs) (See Storey and Tibshirani PNAS 2003; 100:9440-5). I am interested in learning if there is any consensus as to how many features (ie. how many P values) need to be studied before reasonably reliable FDRs can be derived. Does anyone know of a citation where this is discussed? Bill Dupont William D. Dupont phone: 615-...

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 but this is different from plot estimated probability. There is one function pamr.xl.plotcvprob.compute...

Dear Dr. Graves Many thanks for your response. FDRs and their associated q values do differ from Type I error rates and P values (See Storey and Tibshirani PNAS 2003;100:9440-5). It is an approach that is rapidly gaining popularity in the analysis of genomic data where we have massive numbers of covariates measured on a comparatively modest number of subjects. To my mind it is a real advance in dealing with the extreme multiple comparisons problems that...

...nents. The package's algorithms are built on top of these functions. At the moment, algorithms are provided for particle filtering (AKA sequential importance sampling or sequential Monte Carlo) and the likelihood maximization by iterated filtering (MIF) method of Ionides, Breto, and King (PNAS, 103:18438-18443, 2006). Future support for a variety of other algorithms is envisioned. A working group of the National Center for Ecological Analysis and Synthesis (NCEAS), "Inference for Mechanistic Models", is currently implementing additional methods for this package. Simple work...

...nents. The package's algorithms are built on top of these functions. At the moment, algorithms are provided for particle filtering (AKA sequential importance sampling or sequential Monte Carlo) and the likelihood maximization by iterated filtering (MIF) method of Ionides, Breto, and King (PNAS, 103:18438-18443, 2006). Future support for a variety of other algorithms is envisioned. A working group of the National Center for Ecological Analysis and Synthesis (NCEAS), "Inference for Mechanistic Models", is currently implementing additional methods for this package. Simple work...

...I'm curious about support for satnav (PNA) devices by the proprietary support programs they use for updating maps, etc. The AppDB shows that TomTom Home doesn't currently work, but what about the support programs for the raft of cheap WindowsMobile devices, e.g. the Binatone X.350 or Mio PNAs. I can't find any mention of them in AppDB. Martin

Hello to everyone! I have built CRAN task view for genetics. For now I have not submit it to CRAN yet and it can be accessible from: http://www.bfro.uni-lj.si/MR/ggorjan/software/R/Genetics.html http://www.bfro.uni-lj.si/MR/ggorjan/software/R/Genetics.ctv I have not submitted it to CRAN, since I would like first some opinion about it. Genetics is really so broad field that I belive one person

I am trying to install two R packages to produce cartograms like in the work of Gastner and Newman: http://www.pnas.org/content/101/20/7499.full.pdf but I have a problem installing Rcartogram and rdyncall packages. Both are not available in CRAN and have to be installed from archivea and produce errors: > install.packages("C:/Users/Milena/Downloads/*Rcartogram*_0.2-2.tar.gz", > repos = NULL, t...

Hi I have a matrix with 30 observations and roughly 30000 variables, each obs belongs to one of two groups. With svm and slda I get into memory troubles ('cannot allocate vector of size' roughly 2G). PCA LDA runs fine. Are there any way to use the memory issue withe SVM's? Or can you recommend any other classification method for such huge datasets? P.S. I run suse 9.1 on a 2G RAM

I''m a newbie attempting to get a custom fact distributed to clients. I''ve followed the instructions at http://reductivelabs.com/trac/puppet/wiki/AddingFacts and based my first fact on a simple recipe. I''m having at least one problem and possibly more. 1) Puppet/facter fails to load the custom fact, complaining that "non- sh interpreters are not currently

Hello developers folks! First, congratulations for the wonderful work with R. For science, barplots with error bars are very important. We were wondering that is so easy to use the boxplot function: boxplot(Spores~treatment, col=treatment_colors) But there is no such function for barplots with standard deviation or standard error. It becomes a "journey" to plot a simple graph (e.g.

In my recent security email, I got the following errors: cantona.dnswatchdog.com login failures: Aug 20 02:37:19 cantona sshd[9444]: fatal: Write failed: Operation not permitted Aug 20 04:30:42 cantona sshd[16142]: fatal: Write failed: Operation not permitted Aug 20 21:21:51 cantona sshd[45716]: fatal: Write failed: Operation not permitted So three questions: What is it? Should I be worried?

Hi everyone, first of all, I would like to say that I am a newbie in R, so I apologize in advance if my questions seem to be too easy for you. Well, I'm looking for periodicity in histograms. I have histograms of certain phenomenons and I'm asking whether a periodicity exists in these data. So, I make a periodogram with the function spec.pgram. For instance, if I have a histogram h, I