similar to: Help with lumi package R code

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

To whom it may concern. As I would like to analyse some array data I was keen on downloading the lumi package that depends obviously on hdrcde that is not available for r 2.12.1. I did not find instructions to solve or circumvent this problem. Installing hdrcde by hand did not work either. It was not detected by > (.packages(all.available=TRUE)) if installed in the R library. Thanks Hermann

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>

Dear R gurus, I have a very embarrassingly parallelizable job that I am trying to speed up with snow on our local cluster. Basically, I am doing ~50,000 t.test for a series of micro-array experiments, one gene at a time. Thus, I can easily spread the load across multiple processors and nodes. So, I have a master list object that tells me what rows to pick up for each genes to do the t.test from

Hi, i have two files (file1.txt and file2.txt) which i would like to merge, based on certain criteria, i.e. it combines data based on matching geneID and exons. i have used the merge option, but it does not give me the desired outcome. merged.txt shows the result i would like. *File1. txt* ** AffyProbe ProbeType Flag GeneSymbol GeneID Exons Chrom Strand Affytart AffyEnd 1

Dear all, Here is my code which am using to combine 5th column from different data sets. Here is the function to do my job genesymbol.append.file <-NULL gene.column <- NULL readGeneSymbol <- function(files,genesymbol.column=5){ for(i in fnames){ temp <- read.table(fnames,header=T,sep="\t",stringsAsFactors=F,quote="\"")

Hi, i have two files (file1.txt and file2.txt) which i would like to merge, based on certain criteria, i.e. it combines data based on matching geneID and exons. i have used the merge option, but it does not give me the desired outcome. merged.txt shows the result i would like. *File1. txt* ** AffyProbe ProbeType Flag GeneSymbol GeneID Exons Chrom Strand Affytart AffyEnd 1

I am trying to restart on R after 2 months stop. Start with previously functioning procedure: "ch<-odbcConnect("dBase Files")" get "Warning message: ODBC connection failed in: odbcConnect("dBase Files") " I have tried unsuccessfully different working directories. The only change I see is that I am working with a new login account on the same machine.

Hi all, I am trying to do fitting of large sets of timeseries data, and error messages derail the process when I encounter a dataset that doesn't fit. I'd like to ignore those "misfits" and try another equation or move to the next dataset. Any ideas? (piece of code below) Thanks, --Warren ##The code looks something like this: attach(zf) x <- hours

Hello all! I am currently trying to sort a data frame in a particular way, but I am having some difficulties with this. Specifically I want to sort the below dataset in such a way that there is only one line per ProteinID and if there are multiple GeneID or GeneName entries for a single proteinID, that they be concatenated with a comma separating them. The way I have done it earlier worked fine

I use hierclust (hierarchical clustering) in multiv package. In the documentation it is said that plclust (plotting a dendrogram) is available in S-plus. Can I find it anywhere (I have searched through http://lib.stat.cmu.edu/S and found only quotations of plclust in multiv) or is it only part of the S package (which I don't have)? Thanks --------------- Charles RAUX, Laboratoire

Hi all I am a complete newbie to this list (just subscribed) and a newcomer to R (an S user from olden times). I have been using scatter3d to create a 3d scatter plot with surface. The graphic is created within the rgl package and I have used rgl.postscript to export it so I can generate a publication quality image. My problem is that the plotted surface is no longer transparent in the

A disturbing behaviour of R: an import of data using RODBC library (Windows 98, R 1.1.1) recognizes accented characters in variables names but these can't be manipulated further. See below: > library(Rodbc) > ch<-odbcConnect("Paradox Files") > pollut<-sqlFetch(ch,Pollutio) > pollut Mortalit? Densit? Pollution 1 82 600 110 2 97 960

Hi, maybe someone can help me with this: I have a matrix of genes and values: GeneName Value Abc1 10 Abc2 11 Bbc1 -5 Bbc31 2 Ccd 5 Ccd -2 Ccd 7 Dda 5 Dda 10 ..... ..... Zzz3 -1 I would like to

Dear R-Helpers, I have a data.frame (df) and the head of data.frame looks like ProbeUID ControlType ProbeName GeneName SystematicName 1665 1577 0 pSysX_50_22_1 pSysX_50 pSysX_50 5422 5147 0 pSysX_49_8_1 pSysX_49 pSysX_49 4042 3843 0 pSysX_51_18_1 pSysX_51 pSysX_51 3646 3466 0 sll1514_0_2 sll1514 sll1514

How can I draw a 3D perspective of a contingency table, that is showing 3D bars whose height is in proportion of the table cells? --------------- Charles RAUX, Laboratoire d'Economie des Transports CNRS-Universit? Lumi?re Lyon 2-ENTPE email : charles.raux at let.ish-lyon.cnrs.fr http://www.ish-lyon.cnrs.fr/let -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-

Some naive questions: 1) How to remove a column in a data frame? I expected that rm would work but this is not the case (e.g. rm(dat$yyy) gives Warning message: remove: variable dat$yyy was not found). I only found to assign NULL value (e.g.: dat$yyy<-NULL). Is it the right way? 2) Is the place formerly occupied by dat$yyy automatically gained by R for other uses? 3) If t1 and t2 are 2 only

I have made a cut of a numeric vector and try to plot it. However only half of the x-axis annotations (the labels) appear on the plot, apparently because of the font size. I have tried cex.lab, cex.axis (what is the difference?) etc. The x labels are never printed whatever value I use from 0.0005 to 20. I can't obtain a way to make all the labels appear correctly. Between the short help

I am forwarding to the list a mail that I send to one of the subscribers, related to codecs comparison. Perhaps the material will be helpful to some of you. <p>Regards, <p> ---- Gabriel Bouvigne www.mp3-tech.org personal page: http://gabriel.mp3-tech.org <strong>attached mail follows:</strong><hr noshade> Hello I just looked at your vp3/mp4 comparison. In

Hi, Kind of related to the new R-based 'R CMD build' script being sometimes confused on Windows (as reported here a couple of weeks ago https://stat.ethz.ch/pipermail/r-devel/2010-June/057759.html), I also started to observe that the new R-based 'R CMD check' script gets also confused sometimes on Windows in a random way. It seems that sometimes (maybe 1% of the times) running