similar to: Help with the lumi R package

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 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 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>

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

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

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 Sir/Madam, I found your email address and your correspondence with R-users. I hope you could help me with this question about the function "ur.ers" in the package of "urca". It is an improved unit root test (Elliott et al. 1996 Econometrica). Do you know how to extract the value of the test statistic from the output? The only thing I can get is the print-out of all

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="\"")

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

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

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 R-experts, I have a data file df as the following: genename variable at 1hr variable at 4 hr variable at 10 hr gene1 gene2 . . . gene5000 I would like to have a graph with X-axis as the time point (1hr, 4hr, 10hr), and Y-axis as the value of the variable. So, basically, I want to do a line with the three different values at 1hr , 4hr and 10hr for all the 5000 genes. My purpose is

i'm having problems creating confgi file someone can send me your config in mail body or how is head of config file because i'm receiving the follow message when i type wine wineserver: /$HOME/.wine/config is not a valid registry file wine client error:(nil): recvmsg: Connection reset by peer

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

I've imported a .csv file where character strings that contained accented characters were written as HTML character entities. Is there a function that works on a vector to translate them back to accented (latin1) characters? Some examples: > grep("&", author$lname, value=TRUE) [1] "Fr&egrave;re de Montizon" "Lumi&egrave;re" [3]

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 all, i'm trying to code a tool to get some images from a ogg/theora file .... so basically i need to get a frame and convert to rgb ... and here is my question (sorry, i'm newbe here) ... how to convert a yuv_buffer to a rgb matrix ? i tryied diferent ways but my mistakes are bassically cause i don't understant how yuv_buffer structure works ... anybody can help? thanks a lot.