similar to: qvalue

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"

Dear R users, Having searched the mail archive I think the conclusion was that it is not possible to have a column name when there is only one column in the matrix. But I thought I'd check with the more experienced users. What I tried to do was: in a loop I pick a column, record the column name and remove the column from the matrix. But when there were 2 columns left, after one column was

Hello I can''t manage to install VB on osx via puppet and pkgdmg provider. puppet client : 2.6.8 on osx snow leopard 10.6.7 puppetmaster : 2.6.8-1~bpo60+1 on debian squeeze The puppet logs say : [...] debug: Puppet::Type::Package::ProviderPkgdmg: Executing ''/usr/bin/curl -o /tmp/VirtualBox-4.0.8-71778-OSX.dmg -C - -k -s --url

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]]

On 5/2/07, r-help-request@stat.math.ethz.ch < r-help-request@stat.math.ethz.ch> wrote: > > Send R-help mailing list submissions to > r-help@stat.math.ethz.ch > > To subscribe or unsubscribe via the World Wide Web, visit > https://stat.ethz.ch/mailman/listinfo/r-help > or, via email, send a message with subject or body 'help' to >

Hi, I'm running the following code to produce lattice plots of microfibril angle versus ring number in Scots pine. There are 12 trees and 5 sample positions ("Position") in each tree: xyplot(MFA ~ RN | Tree, data = MFA.data, groups = Position, subscripts=TRUE, auto.key=list(space = "top", points = FALSE, lines = TRUE, reverse.rows=TRUE,

I couldnt find a previous posting on this in the archives, maybe it has already been mentioned. If you use a calculation to generate n observations in random number generators and you don't round to the nearest integer you may be generating n-1 numbers not n numbers as you thought depending on the storage precision of the calculation. e.g. > m <- 1000 > pi0 <- 0.9 >

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

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

Hello all, I'm trying to use the package qvalue. Upon trying to install it I'm running into trouble. I re-downloaded and installed the most recent CRAN distribution of R which announced itself to have tcltk included. Now when I try to load qvalue I'm getting errors that seem to indicate that I need tcltk2. I tried going to get that package and loading it but both qvalue and tcltk seem

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 all, I want to draw a histgram for each row of a matrix and compare them. However the plot I got does not have the same y range and x range, which makes it difficult to make the comparison. Is there a easy way to fix the x range and y range in a xy plot for several plots, instead of specifying them for each plot. The following is my code for generalizing the matrix and draw the histogram.

Dear all, I need to do some calculation where the code used are below. I get error message when I choose k to be large, say greater than 25. The error message is "Error in integrate(temp, lower = 0, upper = 1, k, x, rho, m) : the integral is probably divergent". Can anyone give some help on resolving this. Thanks. Hannah m <- 100 alpha <- 0.05 rho <- 0.1 F0

Mark, there is a fdr website link via Yoav Benjamini's homepage which is: http://www.math.tau.ac.il/%7Eroee/index.htm On it you can download an S-Plus function (under the downloads link) which calculates the false discovery rate threshold alpha level using stepup, stepdown, dependence methods etc. Some changes are required to the plotting code when porting it to R. I removed the

You asked the same question on the Bioconductor mailing list back in August. At that time, you suggested yourself a solution for how the adjusted p-values should be interpreted. I answered your query and told you that your interpretation was correct. So I'm not sure what more can be said, except that you should read the article Wright (1992), which is cited in the help entry for p.adjust(),

Complains about missing Int16 functionality. So for 64bit on Arm you have to compile without –enable-neon and that has a huge effect on the AEC functionality. The Pi3 with neon is just struggling with the AEC routines as its audibly better on a Pi4 but its not the garble that a Pi0 produces. Without the neon on the Pi3 the 1.2 – 1.85 perf boost of neon with FFT is lost and it really effects AEC

Hello, I am trying to simulate 10 relicates of 100-tables. Each table is a 2 x 3 and 80% pf the tables are true nulls and 20% are non-nulls. The nulls follow the Hardy Weinberg distribution (ratio) 1:2:1. I have the code below but the p-values are not what I am expecting. I want to use the Cochran Armitage trend test to get the p-values. num.reps=10 num.vars=1000 pi0 = 80 num.subjects = 100

Hi, I'm announcing two new releases of opus, along with the first release of the new libopusenc library. First for opus, we just fixed a bad bug in the surround encoding code that would cause very bad quality on signals beyond a certain amplitude. Thanks to Franziska Trojahn and others from HfT Leipzig for finding this issue through their listening test[1] (the quality of the two bad files

Hi, I've just started using R and fdrtool, and I'm not sure if the qvalues I'm receiving back are accurate. I performed fdrtool on pvalues obtained from a two way anova on proteomics data. So I have 266 data values (protein spots) for two factors (ft, vr, and the interaction) for each biological sample. One of the two factors (vr) has a highly significant effect with 119 protein