search for: fdrtool

Hello, I am using fdrtool(x, statistic="pvalue") where x is a vector of chisq p-values. I can get this command to work with some x, but not with others. When it does NOT work, I get the following screen output: > fdrtool(pvals$Chi2.pval, statistic="pvalue") Step 1... determine cutoff point Step 2... e...

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)...

...My problem is that I need to use a function and the output is a vector of only the non NA values, so shorter than the list I would obtain dropping the data.frame. What is the cleanest way to keep row and column names or putting the values back into the same data frame format? The function is fdrtool() and I can compute the values I'm interested like this: FDR=fdrtool([!is.na(zscores)])$qval But at this point I don't know how to track back these values, to the original data frame Thanks, Gian Luca

I'm using the monoreg function (with weights) from the fdrtool package. How can I calculate the R square for this type of regression? Thanks for your help, Thierry -- View this message in context: http://www.nabble.com/R-square-for-Monotone-regression-tp15580803p15580803.html Sent from the R help mailing list archive at Nabble.com.

...old definition of det() ## det.matrix <- det det <- function(x, ...) UseMethod("det") det.default <- base::det which allows me perfectly fine to use det() as determinant of a matrix, but still loading the library complains with a > library(sretools) Loading required package: fdrtool Attaching package: 'sretools' The following object(s) are masked from package:base : det Is there a recommended way to do this style of "overloading" (albeit a completely different kind of function), or am I simply not supposed to use the name of an existing function in my...

...'devtools', 'digest', 'diptest', 'doBy', 'DoE.wrapper', 'e1071', 'effects',   'ENmisc', 'epiR', 'eRm', 'evaluate', 'evd', 'FactoMineR', 'fArma', 'fAssets', 'fBasics', 'fdrtool',   'fExoticOptions', 'fExtremes', 'fGarch', 'fields', 'flexclust', 'fMultivar', 'fNonlinear', 'fOptions',   'forecast', 'foreign', 'fpc', 'fracdiff', 'fRegression', 'FrF2', 'FrF2...

...bit version) packages: see below... Package Version brew "brew" "1.0-3" colorspace "colorspace" "1.0-1" corpcor "corpcor" "1.5.6" digest "digest" "0.4.2" fdrtool "fdrtool" "1.2.6" GeneCycle "GeneCycle" "1.1.1" ggplot2 "ggplot2" "0.8.7" longitudinal "longitudinal" "1.1.5" MASS "MASS" "7.3-6" plyr "plyr&quo...

...="\"") > ct<-t(ctraw) > ftraw<-read.csv("ft.csv", header = TRUE, sep = ",", quote="\"") > > ft<-t(ftraw) > library(GeneCycle) Loading required package: longitudinal Loading required package: corpcor Loading required package: fdrtool Loading required package: locfdr Loading required package: splines > ctgtest<-fisher.g.test(ctanalysis) Error in r[i1] - r[-length(r):-(length(r) - lag + 1)] : non-numeric argument to binary operator [[alternative HTML version deleted]]

I have recently upgraded to Ubuntu Gutsy and, for the first time, am using a 64-bit installation. After failing miserably to install R from source, not a problem for me in the past with a 32-bit install, I went the route of using the Debian Etch build. This went smoothly, but I am unable to update my numerous R and BioConductor packages, getting non-zero exit status errors on each package. Is