search for: siggen

Displaying 18 results from an estimated 18 matches for "siggen".

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2011 Feb 09
1
samr - extract genes from siggenes.table
...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....
2010 May 25
1
doubt about samr siggenes.table$genes.up
Hi, here's my siggenes.table$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" "...
2007 Aug 20
0
trouble extracting R code from vignette using example from www.bioconductor.org
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 ins...
2004 Nov 22
1
Questions of Significance Analysis of Microarrays(SAM){siggenes}
......) 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,...
2006 Nov 18
1
Why SAM has totally diffent results in R2.1.1 and R2.4.0
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...
2005 Dec 26
0
problem with samr
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) t...
2007 Jan 23
3
the value of Delta
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 Ass...
2012 Mar 30
1
Help with the lumi R package
...## 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]]
2012 Mar 30
0
Help with lumi package R code
...## 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]]
2006 Sep 14
1
EBAM ERROR
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 poin...
2006 Apr 27
0
pamr package: pamr.adaptthresh() error rates
...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 = &quot...
2006 Apr 27
0
package pamr: pamr.adapthresh() ---- Take 2!
...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 = &quot...
2006 Sep 14
0
Help On EBAM
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 poin...
2005 Oct 07
0
Differentially expressed gene list
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...
2009 Mar 31
2
How to generate natural cubic spline in R?
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?
2007 Nov 02
0
loading installes package including all needed subpackages
...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...
2007 Oct 30
6
trouble installing building packages from source using R 2.6.0 on Ubuntu Gutsy AMD64
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
2005 Sep 24
1
Encrypt some services with ipsec
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