similar to: the value of Delta

Hi BioC user, I have a problem extracting the gene set I would like to work with. Here is I work with my data: normData <- read.delim("normalizedData.txt",sep ="\t") ######### two class unpaired comparison # y must take values 1,2 classes <- c(-1,-2,1,2) #prepere the data for the samr analysis data.x <-as.matrix(normData[,8:11]) d=list(x=data.x,y=classes,

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 know what is going on? Thanks for any suggestions.

Dear R community members, I think I am asking a very simple question, but I really looked up in the faqs and manuals and found nothing helpful. I am trying to plot a data frame with the following structure (this is just a small extract): glo conc odor line series X1 X2 X3 X4 X5 X6 X7 X8 X9 X10 X11 X12 X13 1 0 AIR LN1 UP -0.488

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" "RPL15P22" "-1.44115338424578" "-18"

we are migrating our standalone Samba sever (3.0.14a) on a Solaris 10 box to an RHEL 6.3 box. Testing shows that on Solaris 3.0.14a works with both the OpenLDAP server we are currently using and the IPA2.2 server as LDAP backend. But 3.5.10-125.el6 on a RHEL 6.3 box does not work with either. I can still map a share with 3.5 as owner of the shared directory, but secondary group ownership does

Dear List, I tested the example in the reposTools vignette: library(reposTools); Loading required package: tools genRepos("Test Repository", "http://biowww.dfci.harvard.edu/~jgentry/","newRepos"); Error in rep.int(colnames(x), nr) : unimplemented type 'NULL' in 'rep' Could someone help me out with this one? I'd appreciate all help.... I am

Hi, After mounting -t ext2 an ext3 partition, working with, do I have to recreate .journal when I remount the partition as ext3 ? Thanks ! Liu

Dear All: Significance Analysis of Microarrays(SAM) As we know sam do multiple t.test as following ## Default S3 method: t.test(x, y = NULL, alternative = c("two.sided", "less", "greater"),mu = 0, paired = FALSE, var.equal = FALSE,conf.level = 0.95, ...) var.equal: a logical variable indicating whether to treat the two variances as being equal. If 'TRUE'

Full_Name: Mike Ulrich Version: 2.9 OS: Mac OSX Submission from: (NULL) (69.169.178.34) The help documentation for loadings() lists more then one parameter. The function call only expects one parameter. The digits, cutoff, and sort parameters are not used in the function. ## S3 method for class 'loadings': print(x, digits = 3, cutoff = 0.1, sort = FALSE, ...) ## S3 method for class

Hi, I am working of Intel 82576 device to test the SRIOV functionality. I want to assign VFs to a VMs(domU) and verify the control and data path. I installed Xen-unstable with 2.6.30-rc3(dom0). But the SRIOV functionality isn''t working, because MSI is not supported. Please let me know, what version of Xen and dom0 supports above functionality? Is there any tool available to manage SRIOV

Hello, I am not sure about the p.adjust( , fdr). How do these adjusted p-values get? I have read papers of BH method. For independent case, we compare the ordered p-values with the alfa*i/m, where m is the number of tests. But I have checked that result based on the adjusted p-values is different with that by using the independent case method. Then how do the result of p.adjust( , fdr) come? And

This is better suited to llvm-dev, so I'm directing it there. From: llvm-commits <llvm-commits-bounces at lists.llvm.org> on behalf of Qing Shan Zhang via llvm-commits <llvm-commits at lists.llvm.org> Reply-To: Qing Shan Zhang <qshanz at cn.ibm.com> Date: Sunday, August 19, 2018 at 10:10 PM To: "llvm-commits at lists.llvm.org" <llvm-commits at lists.llvm.org>

Dear Users, I ran factor analysis using R and SAS. However, I had different outputs from R and SAS. Why they provide different outputs? Especially, the factor loadings are different. I did real dataset(n=264), however, I had an extremely different from R and SAS. Why this things happened? Which software is correct on? Thanks in advance, - TY #R code with example data # A little

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 =

Hi Steven, I onced played with your PV-on-HVM driver before it is checked in into unstable, I remember at that time, there is a XENFEAT_64bit_shared_info flag to handle situation of 32bit guest on 64bit hypervisor, at least vnif works fine with it. Later, when the code is checked in, this flag is gone. At first I though this was an effort to make hypervisor more transparent to HVM guest, but now

Hi, With kernel 2.4.10, when I do $ mkdir foo; cd foo; rmdir ../foo; ls then ls becomes zombie. $ ps xau|grep ls liu 596 0.0 0.0 148 88 ? D 12:03 0:00 ls This does not happen with 2.4.10 on an ext2 filesystem, nor with 2.4.9/ext3. The command cd instead of ls is OK. Distribution is Slackware 8.0 and the kernels are stock ones. Liu

Hi all, My name is Amy, I am a masters student in Bioinformatics at North Carolina State University. I am working on a project and I am trying to use the lumi R package for microarray data analysis. I have shown the sample code here and have questions about modifying the sample code for my own data. lumi package in R, example.lumi, the sample data has 8000 features and 4 samples I have

Dear list members, I apologize for putting this (probably) very basic question on the mailing list. I have scanned through the R website (using search) but did not found an answer. (code included below) A factor matrix is simply extracted (which can then subsequently be exported using write.table) by FACT$loadings[1:6,]. I would also like to specifically extract and export

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

I am having difficulty obtaining the scores from my principal component analysis. I have used this method before and have had no problems. The data set that I am using this time is similar to what I have used in the past. What do I need to do to my dataset in order for me to obtain these scores? R screen says the following message Error in factanal(covmat = pasa.cov, factors = 4) :