similar to: trouble installing qvalue package

I am using storey's qvalue package but I keep on getting errors. Why is this? > qvalue(p, lambda=0.5)$pi0 [1] "ERROR: p-values not in valid range." Error in qvalue(p, lambda = 0.5)$pi0 : $ operator is invalid for atomic vectors -- Thanks, Jim. [[alternative HTML version deleted]]

Good Morning Everyone, I was going through my list of FTBFS packages today and I fixed all my R packages but 2: qvalue and xtable. qvalue requires ggplot2 xtable requires: lsmeans, spdep, splm, sphet, plm I am not doing any R anymore these days and in fact spot has been the one maintaining most of my R packages these days (thanks spot!!), so I am not really interested in maintaining more R

Dear colleagues, This is not strictly a R question, but I hope it is ok to ask on the list. I fed a vector of p-values from about 20 million anova tests to the package q-value and obtained this output: > qsummary(asso_p.qvalue) Call: qvalue(p = asso_p.vec) pi0: 1 Cumulative number of significant calls: <1e-04 <0.001 <0.01 <0.025 <0.05 <0.1 <1

Dear All, In Storey's estimator of the proportion of true nulls, the estimator depends on the tuning parameter lamda. Suppose now that an estimator of this proportion has been obtained by the qvalue package, what is the lamda that corresponds to the estimate? How to get this lamda? Thanks, -Chee [[alternative HTML version deleted]]

Had some packages fail install so I updated to today's R-beta release. On updating packages the following packages still fail. sessionInfo follows. Mark Warning messages: 1: In install.packages(update[instlib == l, "Package"], l, contriburl = contriburl, : installation of package 'MANOR' had non-zero exit status 2: In install.packages(update[instlib == l,

Hi, I get the following error when trying to load the BiodiversityR package > library(> library(BiodiversityR) Loading required package: tcltk tcltk DLL is linked to '/opt/X11/lib/libX11.6.dylib' Error: package or namespace load failed for ?tcltk?: .onLoad failed in loadNamespace() for 'tcltk', details: call: fun(libname, pkgname) error: X11 library is missing: install

Dear R users I would like to simulate underdispersed Poisson and binomial distributions somehow. I know you can do this for overdispersed counterparts - using rnbinom() for Poisson and rbetabinom() for binomial. Could anyone share functions to do this? Or please share some tips for modifying existing functions to achieve this. Thank you very much for your help and time Shinichi

Hi, I am trying to connect points on a graph that originate from *different columns of data*. For each sample I have minimum and maximum data points and I would like to draw a line connecting these in order to visualize the spread, as well as where each sample is in relation to the x-axis. So far I can generate the points, but the only lines I have been able to make join all the minimum values

A package I have written makes considerable use of external C code. There appear to be no problems building a Windows binary with the GNU C compiler, but now I would like to make the package available for other platforms. A stringent check of the code with the gcc options '-Wall -pedantic' flags many nested functions and variable-length arrays that are not allowed in ISO C. Is it

I am having problems getting my app to run under wine-git so that I may perform my regression. Here is the output when I run wine-git/wine: Code: Wine cannot find the FreeType font library. To enable Wine to use TrueType fonts please install a version of FreeType greater than or equal to 2.0.5. http://www.freetype.org Wine cannot find the FreeType font library. To enable Wine to use TrueType

Hello, I installed Wine today using the instructions on the osxwinebuilder page: http://code.google.com/p/osxwinebuilder/ All went good, until trying out to launch iexplore, or winecfg or anything else. I get the following error message each time doing the command: wine winecfg or wine iexplore: Code: $ wine winecfg Wine cannot find the FreeType font library. To enable Wine to use TrueType

Dear All I'm logging the stdout and stderr of an R program into two separate files (stderr.txt and stdout.txt) using sink() I would like to append extra information such as "date", "memory usage" etc to every line of output that goes to stdout or stderr. For example > cat("hello \n") should give output that looks something like: "hello --- Thu Jun 19

Hi, All I got trouble on installing the qvalue package. Error message: package 'tcltk' does not have a name space [cchen1 at ibibmem Yale_CB]$ R CMD INSTALL qvalue.tar.gz * installing to library '/cchome/cchen1/R/x86_64-unknown-linux-gnu-library/2.10' * installing *source* package 'qvalue' ... ** R ** data ** inst ** preparing package for lazy loading Error : package

Why is 19 March, 1947 a little longer than one day? x <- as.POSIXct("1947-04-16") julian(x, origin = as.POSIXct("1947-03-20")) Time difference of 27 days julian(x, origin = as.POSIXct("1947-03-19")) Time difference of 28.04167 days > julian(x, origin = as.POSIXct("1947-03-18")) Time difference of 29.04167 days I am running R-1.7.1 compiled on

Dear all I'm building logistic regression models using glm() and then validating their predictive ability on a test set using predict() to get the probabilities. I understand how to attain the deviance of the model fitted to the training set. But is there a way to get the deviance within the test set? Cheers Tom -- Thomas Allen Department of Biochemistry University of Otago 710 Cumberland

Hi, Is there any equivalent of type="n" when constructing barplots which will still construct the axes (plot=F, as it says doesn' plot anything at all). Alternatively I tried setting col="white" and border="white" but the border command does not seem to be operational. True?? Any other ideas? What I'm actually trying to do is construct vertical abline()'s

I have just used the RAqua.pkg to install R, and it doesn't work! I have Mac OS X 10.3, and the old version of R works OK, but the .pkg thing installed, and then when I double-click on the "StartR" application nothing happens. Nothing at all, no little icon bobbing up and down in the dock, just nothing. What have I done wrong? I didn't have to install the other packages

Hello, I'm apologize to have made failure before. I wrote this : p<-scan("teststat.txt") on R and R returns Error in scan ("teststat.txt") : "scan" expected a real, got "x". I don't really understand,because teststat has been created, so........ Thanks a lot. Sandrine

Hi, I saved an image and planed to open it whenever I want to load it. However, when I open it, It doesn't work. The code is following, and saved it as an image. .First<-function(){ require(tcltk) require(TeachingDemos) library(gWidgetstcltk) options(guiToolkit = "tcltk") win <- gwindow("Don't worry", visible = FALSE) } Error message is following, Error :

Dear list, I have been trying to run the function "qvalue" under the package qvalue on a vector with about 20 million values. > asso_p.qvalue<-qvalue(asso_p.vector) Error: cannot allocate vector of size 156513 Kb > sessionInfo() Version 2.3.1 (2006-06-01) i686-pc-linux-gnu attached base packages: [1] "methods" "stats" "graphics"