search for: genesets

Dear Sir/Madam, I found your email address and your correspondence with R-users. I hope you could help me with this question about the function "ur.ers" in the package of "urca". It is an improved unit root test (Elliott et al. 1996 Econometrica). Do you know how to extract the value of the test statistic from the output? The only thing I can get is the print-out of all

hi I have vector test. It has 3 elements. I want to join the three into one vector. "Geneset=HSA04910_INSULIN_SIGNALING_PATHWAY-157- 20". how can i do it. > class(test) [1] "character" > test [1] "Geneset=HSA04910_INSULIN_SIGNALING_PATHWAY" "157" [3] "20" Ramya --

hi there, I want to write the plots in the pdfs and the details about the graph in a seperate notepad. plot(as.numeric(lapply(resultgenes,length)), main= "Geneset.gene#.bias.test",xlab="Top.Ranked.Genesets", ylab="gene.number.per.geneset") lines(loess.smooth(c(1:1000),as.numeric(lapply(resultgenes,length)), span = 2/3, degree = 1, family = "gaussian", evaluation = 50),col=2, lwd=3) i want this graph in the pdf and some notes regarding the graph in a notepad. Kindly he...

Hi, Could you please let me know to use a list in a for loop here geneset is a loop.I am trying to match the names of the list with 1st row of the output. result<- list() for(i in 1:length(output) { result[[i]] <- geneset(which(geneset %n% output[,1])) } Kindly help me out -- View this message in context: http://www.nabble.com/For-loop-tp18163665p18163665.html Sent from the R

hi I want to compare two list by its names and get the values of that list. can anybody let me know the syntax of comparing the list by their names using a for loop c.genes<- list() for(i in 1:100) c.genes[[1]]<- geneset(which(geneset == tobecampared[i])) } here geneset is a list and also tobecampared is a list Thank you Ramya -- View this message in context:

The GeneSetCollection class in the Bioconductor package GSEABase extends 'list' > library(GSEABase) > showClass("GeneSetCollection") Slots: Name: .Data Class: list Extends: Class "list", from data part Class "vector", by class "list", distance 2 Class "AssayData", by class "list", distance 2 If I create

Dear list, I have gene expression measurements obtained by PCR on 11 genes, tabulated as a data matrix. I'm attempting to use GSA package to distinguish any significant changes in these genes as a pathway. My response variable is binary, 0=no disease, 1=disease. I have read the PCR data into R as follows: data <-

Hi All, I want to select rows at random from a large data.frame while achieving a particular distribution defined my a given subset of this data.frame. How can I do this? More details and what I've done so far is given below. I have gene expression data and gene sets of interest. In order to look at enrichment of differential expression I'm doing a simple permutation approach: Selecting

Hi, I have an RData file containing a GeneSetCollection object (Bioconductor), http://www.cs.mu.oz.au/~gabraham/c2.RData. I think it uses lazy loading because packages are only loaded when I access the object (see below) in the R console. When I try the same with Rscript, it segfaults. This happens on 2.9.0 both on Linux and Mac: Rscript -e 'load("c2.RData"); c2[1]' ***

Hi guys, I want to transfer the following code from R into .Call compatible form. How can i do that? Thanks!!! INT sim; for(i in 1:sim){ if(i>2) genemat <- genemat[,sample(1:ncol(genemat))] ranklist[,1] <- apply(genemat, 1, function(x){ (mean(x[cols]) - mean(x[-cols]))/sd(x)}) ranklist <- ranklist[order(ranklist[,1]),]

Has something changed in R that requires an update in the genetics package by Gregory Warnes? I am using R version 2.5.0 This used to work > summary(founders[,59]) to prove that it is a genotype class > class(founders[,59]) [1] "genotype" "factor" Now when I issue the command: > summary(founders[,59]) I get: Error in attr(retval, "which") <- which :

Geneset_name #Chromosome #Hit_in_Biomart original_geneset_len Missing.genes [1,] "AGUIRRE_PANCREAS_CHR12" "1" "51" "59" "8" [3,] "AGUIRRE_PANCREAS_CHR9" "1" "24" "24"