search for: qvalue

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 packa...

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 ** p...

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 packages. Would someone...

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]]

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 wit...

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"...

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 p-value 22711 59067 262103 551316 1013241 1936797 20048103 q-value 3554 5211 9275 12807 16951 24557 20048103 I can see...

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]]

Hi, I am trying to install qvalue, however its giving installation error -> Error : package 'tcltk' does not have a name space ERROR: lazy loading failed for package ?qvalue? * removing ?/home/sbw/R/x86_64-unknown-linux-gnu-library/2.12/qvalue? The downloaded packages are in ?/tmp/RtmpKnS1X4/downloaded_packages? Warn...

Hi, I have a huge dataset (53 million records). I have to calculate the p and q values of my data. How can I do it in R or perl? I have downloaded R (I'm completely new to R). and the package qvalue but I don't understand how can I call/use qvalue package with R. When I type library(qvalue), it gives me an error that this package doesn't exist. What should I do? Thanks! -- View this message in context: http://r.789695.n4.nabble.com/Calculating-p-and-q-values-with-R-tp2341763p2341763.h...

...es: 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, "Package"], l, contriburl = contriburl, : installation of package 'qvalue' had non-zero exit status 3: In install.packages(update[instlib == l, "Package"], l, contriburl = contriburl, : installation of package 'tkWidgets' had non-zero exit status > sessionInfo() R version 2.6.0 beta (2007-09-18 r42895) i686-pc-linux-gnu locale: LC_CTYPE=en...

panel.lmline returns intercept and slope of y ~ x subsetted to the combination of conditioning factors given to xyplot in lattice. for instance: xyplot(Xvalues ~ log(Qvalues)|Tfac, data = df7, panel = panel.lmline) I am looking to find the equivalent formulation for lm() proper. If I do this: lmcal <- lm(Xvalues ~ log(Qvalues):Tfac, data = df7) Only one value of the intercept is returned. It appears as all the 'individual' intercepts are summed to form...

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 all, apologies if this has been answered before, I didn't find the answer in the archives. I am putting together a package that I would like to have optional functionality if another package is installed. In normal, non-package code, I would simply write something like if (require(qvalue)) { # use package qvalue } else { # do not use package qvalue } If I do something like that in a package, I get warnings about using undeclared imports. In the DESCRIPTION file, I can specify the following fields: Depends : not useful for this purpose Imports : doesn't seem to be usefu...

...when Time, DateTime then "''#{value.strftime("%Y%m%d %H:%M:%S")}''" when Date then "''#{value.strftime("%Y%m %d")}''" when String, ActiveSupport::Multibyte::Chars qvalue = super qvalue = "N#{qvalue}" if !column.nil? && column.sql_type =~ /\Anvarchar/ qvalue else super end end This passed the several tests I wrote for it and otherwise seemed to pass the couple of AR tests I ran against it...

Hi, Dear all, i encounted a problem with tcl/tk installation actually i want to install q-value package i use the R CMD INSTALL command: [root@bioinfo ~]# R CMD INSTALL qvalue_1.20.0.tar.gz * Installing to library �usr/local/lib64/R/library� * Installing *source* package ‘qvalue�... ** R ** data ** inst ** preparing package for lazy loading Error in firstlib(which.lib.loc, package) : Tcl/Tk support is not available on this system Error : package 'tcltk'...

...ortion of false discoveries is 5%. e.g. n <- 1000 pi0 <- 0.5 x <- rnorm(n, mean=c(rep(0, each=n*pi0), rep(3, each=n - (n*pi0)))) p <- 2*pnorm( -abs(x)) p <- sort(round(p,3)) p.adjusted <- p.adjust(p, method="fdr") # Controlling fdr at Q, and p.adjust at level alpha Qvalue <- alpha <- 0.05 threshold <- fdr(p, Q=Qvalue, method="stepup") # fdr function available from the website link above threshold plot(p, p.adjusted) abline(v=threshold, lty=2) abline(h=alpha, lty=2) > # Stepup FDR control at Q=0.05 > sum(p <= threshold) [1] 372 &g...

I am posting this to both R and BioC communities because I believe there is a lot of confusion on this topic in both communities (having searched the mail archives of both) and I am hoping that someone will have information that can be shared with both communities. I have seen countless questions on the BioC list regarding limma (Bioconductor) and its calculation of FDR. Some of them involved

I am posting this to both R and BioC communities because I believe there is a lot of confusion on this topic in both communities (having searched the mail archives of both) and I am hoping that someone will have information that can be shared with both communities. I have seen countless questions on the BioC list regarding limma (Bioconductor) and its calculation of FDR. Some of them involved

...ttp://www.bioconductor.org/packages/2.6/bioc/bin/windows/contrib/2.11/SSPA_1.4.0.zip' Content type 'application/zip' length 305310 bytes (298 Kb) opened URL downloaded 298 Kb package 'SSPA' successfully unpacked and MD5 sums checked > library(SSPA) Loading required package: qvalue Loading required package: tcltk Loading Tcl/Tk interface ... done Error : .onAttach failed in attachNamespace() for 'SSPA', details:   call: fun(...)   error: could not find function "addVigs2WinMenu" Error: package/namespace load failed for 'SSPA' > sessionInfo() R ve...