search for: siggene

...data.x <-as.matrix(normData[,8:11]) d=list(x=data.x,y=classes, geneid=as.character(normData[,1]),genenames=as.character(normData[,1]), logged2=TRUE) samr.obj<-samr(d, resp.type="Two class paired", nperms=100) delta.table <- samr.compute.delta.table(samr.obj) delta=0.4 siggenes.table<-samr.compute.siggenes.table(samr.obj,delta, d, delta.table,min.foldchange=2) genes.up <- as.data.frame(siggenes.table$genes.up) genes.down <- as.data.frame(siggenes.table$genes.lo) the data set I am working with has four column of two experiments. when running the samr.c...

Hi, here's my siggenes.table$genes.up snippet. Two class unpaired SAMR analysis. "Row" "Gene ID" "Gene Name" "Score(d)" "Numerator(r)" "Denominator(s+s0)" "Fold Change" "q-value(%)" "1" "25" "RPL15P22" "R...

Not sure if this is an R or BioC question so will cross-post. I cannot extract R code from vignettes because system.file("doc", "my.bioc.package") returns "". I got this code directly off of http://www.bioconductor.org/docs/vignettes.html. A specific example using siggenes follows but I have tested this using multiple packages, including those for which I can clearly see the vignette *.Rnw in the doc directory. One thing in my setup that I have customized, and which I wonder if is causing this problem, is that I am using a site-library as directed in the R inst...

......) var.equal: a logical variable indicating whether to treat the two variances as being equal. If 'TRUE' then the pooled variance is used to estimate the variance otherwise the Welch (or Satterthwaite) approximation to the degrees of freedom is used. We are curious why sam in package siggenes do not have var.equal option ? Are there some reason ? sam(data,cl,B=100,balanced=FALSE,mat.samp=NULL,delta=(1:10)/5,med.fdr=TRUE,s 0=NA,alpha.s0=seq(0,1,.05),include.s0=TRUE,p0=NA,lambda.p0=1,vec.lambda.p0=( 0:95)/100, na.rm=FALSE,graphic.fdr=TRUE,thres.fdr=seq(0.5,2,0.5),ngenes=NA,iteration=3,...

Hi, I am using SAM (from siggenes_1.2.11 package) method to select genes from a microarray data set. After installing the latest R2.4.0 on my computer, to my surprise the results are totally different from that calculated using R2.1.1. Even the example code doesn't work the same way under these two versions of R. Does anybody...

Hello Everybody, I am trying to perform SAM with the samr package. I am using the following code: sink ("R005") library(siggenes) library(samr) library(nnet) A <- as.matrix(read.table("D:\samrgenes1000.txt")) B <- as.matrix(read.table("D:\genenames1000.txt")) y1 <- c(rep(1,20),rep(2,6)) #there are 20 chips of one kind and 6 of the other kind. datasam = list(x=A,y=y1,genenames=B,logged2=TRUE) te...

Dear all, I am running R 2.4.1. > library(siggenes); > library(multtest); > cl<-rep(c(0,1),c(3,3)); > sub<-exprs(AffyExpData[,c(1:3,7:9)]); > gn<-geneNames(AffyRAwData); > sam.out<-sam(sub,cl,rand=123,gene.names=gn); We're doing 20 complete permutations > sam.out SAM Analysis for the Two-Class Unpaired Case Assu...

...## print the top 10 genes print(topTable(fit, coef='95:5-100:0', adjust='fdr', number=10)) ## get significant gene list with FDR adjusted p.values less than 0.01 p.adj <- p.adjust(fit$p.value[,2]) sigGene.adj <- probeList[ p.adj < 0.01] ## without FDR adjustment sigGene <- probeList[ fit$p.value[,2] < 0.01] } -- - Amy W. -- Minyue Wang (Amy) Graduate student, Bioinformatics mwang3@ncsu.edu 919-5210893 [[alternative HTML version deleted]]

...## print the top 10 genes print(topTable(fit, coef='95:5-100:0', adjust='fdr', number=10)) ## get significant gene list with FDR adjusted p.values less than 0.01 p.adj <- p.adjust(fit$p.value[,2]) sigGene.adj <- probeList[ p.adj < 0.01] ## without FDR adjustment sigGene <- probeList[ fit$p.value[,2] < 0.01] } [[alternative HTML version deleted]]

Dear RUsers, I am new to R. I am learning how to use R. I am a PC user and run R on windows. I would appreciate if some one could guide me on a few questions I have: 1) I have 4 cel files (2 replicates for NORM and Disease resp). I have been able to run siggenes on this dataset where I have 4 labels in the class file groupsnhi.cl op-> (0,0,1,1) and my data has been read into datrmanhi after performing rma. When I run these commands here I receive these errors: > plot(samnhi.out,seq(0.1,0.6,0.1)) > identify(samnhi.out,ll=FALSE) warning: no point...

...s for 'ntries', and 'reduction factor' in pamr.adaptthresh(), without any success. I have reproduced my code below. Any comments would be appreciated! thanks. ########################### CODE ################################# library(multtest) # golub library(siggenes) # SAM library(e1071) # support vector m/c library(base) library(graphics) library(pamr) library(bootstrap) rm(list = ls()) gc() makeColon <- function(){ # This dataset has 24 cancer, and 9 normal samples n2 <- read.table("data/Colon.data",header = FALSE,sep = "...

...s for 'ntries', and 'reduction factor' in pamr.adaptthresh(), without any success. I have reproduced my code below. Any comments would be appreciated! thanks. ########################### CODE ################################# library(multtest) # golub library(siggenes) # SAM library(e1071) # support vector m/c library(base) library(graphics) library(pamr) library(bootstrap) rm(list = ls()) gc() makeColon <- function(){ # This dataset has 24 cancer, and 9 normal samples n2 <- read.table("data/Colon.data",header = FALSE,sep = "...

Dear RUsers, I am new to R. I am learning how to use R. I am a PC user and run R on windows. I would appreciate if some one could guide me on a few questions I have: 1) I have 4 cel files (2 replicates for NORM and Disease resp). I have been able to run siggenes on this dataset where I have 4 labels in the class file groupsnhi.cl op-> (0,0,1,1) and my data has been read into datrmanhi after performing rma. When I run these commands here I receive these errors: > plot(samnhi.out,seq(0.1,0.6,0.1)) > identify(samnhi.out,ll=FALSE) warning: no point...

Hi,when I perform SAM on my array data(siggenes)I have some problems in retrieving the separate lists of up regulated and down regulated genes. When I write: fold<-function(x){ gruppi<-split(x,controllo) geni1<-abs(mean(gruppi[[2]])-mean(gruppi[[1]])) return(geni1) } fold<-esApply(expr.contr.tratt.4,...

Suppose I have two var x and y,now I want to fits a natural cubic spline in x to y,at the same time create new var containing the smoothed values of y. How can I get it?

...Discriminant Analysis Rgraphviz Provides plotting capabilities for R graph objects ROC utilities for ROC, with uarray focus rpart Recursive Partitioning RSQLite SQLite interface for R siggenes Multiple testing using SAM and Efron's empirical Bayes approaches simpleaffy Very simple high level analysis of Affymetrix data sma Statistical Microarray Analysis spatial Functions...

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

Hi all, I have two prodction servers with FreeBSD 5.4 (all security patches are applied). They running some services like dns, ssh, http, ftp, etc. But I woukd like to encrypt some services for some hosts with ipsec when it is accessed. For example: - DNS resolution: not encrypted. - DNS replication master-slave: encrypted by ipsec. - Telnet: encrypted by ipsec for some hosts. Deny