similar to: about vsn

Could anyone please explain to me why the following writes nothing into "all.Rout" file? If the "for" loop is removed, t.test output can be written into "all.out". Thanks in advance. Minghua Yao ...... zz <- file("all.Rout", open="wt") sink(zz) for(i in 1:n) { Cy3<-X[,2*i-1]; Cy5<-X[,2*i]; t.test(Cy3, Cy5)

Hi, I'm working with custom slides(Cy5) and working in the normalization of the arrays. I have three arrays (technical replicates). I have sucesfully normalized the data using vsn, however i would like to normalize using spike in controls. My controls are annotated as CTL-1 to x and i would like to do etiher a normalization by block per array or the mean of all the controls per array. The gal

Hi, I have some microarray data, cy5 and cy3 values are in log2. Is there a way to check they have undergone lowess normalization ? Thanks Stanley [[alternative HTML version deleted]]

I would like to announce that my DataLoad utility which can be found at: http://www.vsn-intl.com/genstat/downloads/datald.htm has been updated to support R data.frames. DataLoad reads a large variety of data formats (listed on the web page) and can convert these to ASCII or XDR data.frames. Only the Windows and Linux versions are up to date due to the fact that I no longer has access to a Unix

I would like to load ApoAI.RData. During the operation of reading this data an error occurs. There is also a problem with STF file. > library (limma) > load("ApoAI.RData") Warning message: 'RG' looks like a pre-2.4.0 S4 object: please recreate it > objects() [1] "RG" > names(RG) [1] "R" "G" "Rb"

Hello, I am not only interested in finding out which genes are the most highly up- or down-regulated (which I have done using the linear models and Bayesian statistics in Limma), but I also want to know which genes are consistently highly transcribed (ie. they have a high intensity in the channel of interest eg. Cy5 or Cy3 across the set of experiments). I might have missed a straight forward

Dear R-Help, I am using the LIMMA User's Guide 5 January 2007 PDF version. For the example show in Section 7.4 DIRECT TWO-COLOR DESIGNS (pgs. 33-34), I could not grasp the rationale in developing the contrast.matrix with these R statements (">" indicates the R command prompt): > contrast.matrix <-

Dear all, I need some help on matrix design and B statistics by using limma package. I want to compare gene expression in 2 groups of cDNA samples. The experiment compares 4 treated mice(#1,#2,#3,#4) and 4 control mice (#5,#6,#7,#8). The target file is FileName Cy3 Cy5 mice1.spot Control_#5 Treat_#1 mice2.spot Treat_#1 Control_#5 mice3.spot Control_#6 Treat_#2

Dear list members, I am analysing my microarray data using limma package. Now I encounter several problems. Looking forward to your suggestions! Question 1: During the process of background correction using method="normexp", four warning messages appeared as "NaNs produced in: log(x)" (as you can see in the program posted below). What does that mean? How will it effect the

Hi, I have a rather complex xml document that I am attempting to parse based on attributes: <Manifest xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"> <!-- eName : name of the element. eValue : value of the element. --> <OutputFilePath>D:\CN_data\Agilent\Results\</OutputFilePath> <FilesList> <File>

Source: xen Version: 4.17.3+10-g091466ba55-1 Severity: serious Tags: patch pending sid trixie Justification: library ABI skew on upgrade User: debian-arm at lists.debian.org Usertags: time-t NOTICE: these changes must not be uploaded to unstable yet! Dear maintainer, As part of the 64-bit time_t transition required to support 32-bit architectures in 2038 and beyond

The Bioconductor development team announces release 1.2 of the Bioconductor packages for the analysis of genomic data. Bioconductor is an open source bioinformatics software project based on the R language. Version 1.2 features: ===================== * All packages from the 1.1 release are included. All current bug fixes have been applied, and most have been upgraded and provide enhanced

Dear all, I have a question about limmaGUI that is usually run in R environment. My problem is loading data into the programm. I have 6 gpr files that apparently are not compatible with limma. Everytime I'm trying to load the data (including a RNA targets file, an error appears:Error reading files. that I'm not sure,but seems to have something to do with the format of my files

Hi, I have a question concerning the analysis of some affymetrix chips. I downloaded some of the data from GEO GSE11324 (see below). In doing so I'm stuck after I identified the probesets with significant changes. I have problems in assigning probeset specific gene names as well as getting the genomic coordinates. Furthermore I have no clue how to deal with the fact, that most genes have

Hello sir: As to the 2*2 table format for reporting results comparing a new test to true diagnosis,when I got the sensitivity and specificity,how can I calculate the exact 95% confidence intervals (based on the binomial distribution) for sensitivity and specificity via R? Thanks a lot! My best! ------------------------------ ******************************************* Xin Meng Capitalbio

Hello sir: How can I perform McNemar (paired chi square test) by using R? Thanks! ------------------------------ ******************************************* Xin Meng Capitalbio Corporation National Engineering Research Center for Beijing Biochip Technology BioPharma-informatics & Software Dept. Research Engineer Tel: +86-10-80715888/80726868-6438 Fax: +86-10-80726790 Email??xmeng

Hello sir: There are 2 questions about string. 1 How to calculate the width of a string? e.g string "abc"'s width is 3; 2 How can I get the "substring" in such kind of condition: "f:\\JPCS_signal.txt" "f:\\PC1_signal.txt" "f:\\PC2_signal.txt" What I wanna get is "JPCS" "PC1" "PC2".How can I achieve them by R

Neither biocLite nor the GUI menus can install packages on my system. Here is relevant output: > version _ platform i386-pc-mingw32 arch i386 os mingw32 system i386, mingw32 status major 2 minor 11.1 year 2010 month 05 day 31 svn rev 52157 language R version.string R version 2.11.1 (2010-05-31) > source("http://bioconductor.org/biocLite.R") BioC_mirror =

Hi all: I wanna know how to expoort ".xls" file. And in the exported ".xls" file, how to set different cells with different color? Thanks a lot! My best. ------------------------------ ******************************************* Xin Meng Capitalbio Corporation National Engineering Research Center for Beijing Biochip Technology BioPharma-informatics & Software

Hello sir: group1:1,2,3,4 group2:1,3,4,5 group3:2,4,8,9 .. ... group1000:9,3,8,2 I wanna get the "intersection set" and "union set". I've tried command "setdiff"and "union",but only two groups is permited.How can I deal with multi groups to find the "intersection set" and "union set"? Thanks a lot! My best