similar to: Complete newbie - create microarray image from data file?

Hi,   When I check the beadarray in R, I found the following information:   > package.version("beadarray") [1] "1.16.0" > library(beadarray) Error in library.dynam(lib, package, package.lib) : Cannot find sharing library (beadarray)   Does anybody know what I can do for this problem?   Thanks a lot!   Best Shizhu     [[alternative HTML version deleted]]

Dear R users, I am using the beadarray package. I am trying to upload raw bead-level data using these commands: ######################################################## library(beadarray) datadir <- ("C:/Computer_programs/R/beadarray/cecilia") targets = read.table("targets.txt", sep = "\t", header = TRUE, as.is = TRUE) BLData = readIllumina(arrayNames =NULL,

hi I am going to crazy.I want to use beadarray package in R, but I cant. when I want install it, I encounter to this message "Loading required package: hwriter Loading required package: sma Error in library(pkg, character.only = TRUE, logical.return = TRUE, lib.loc = lib.loc) : 'sma' is not a valid installed package" I cant find sma and hwriter packages, it seems that they are

Dear R-experts, My problem is how to handle a 10GB data file containing genotype data. The file is in a particular format (Illumina final report) and needs to be altered and merged with phenotype data for further analysis. PERL seems to be an frequently used solution for this type of work, however I am inclined to think it should be doable with R. How do I open a text-file, line by line,

Hi All: Has anyone analyzed Illumina 550K data using DNAcopy package? I have around 2300 samples. According to Venkatraman and Olshen 2007 paper, it needs about 25 min to run a single sample for Affymetrix 100K. I am afraid it will take too long to analyzed my data. Anybody has an idea? Thanks! Best, -- View this message in context:

Hello everyone, I`m trying to normalize and analize an illumina SNP array. But when i`m trying to segmentate i`m getting an error: Error in sort(abs(diff(genomdat)))[1:n.keep] : only 0's may be mixed with negative subscripts. I`ve tried everything to fix this but the error still occours. Can anybody give me a tip? Thanks in advance! -- View this message in context:

Hi, I have Agilent and Illumina SNP data. That's the only thing I know about the files - there seem to be no version specification in any of them. Is there a generic genotype calling algorithm that I could try to use on these datasets? thanks, N. -- View this message in context: http://www.nabble.com/generic-genotype-calling-algorithm--tp23141124p23141124.html Sent from the R help

Hello Everyone, I am writing programs in R from 7 months and I am able to solve most of the errors/issues except for this current post. My Task is to read a Microsoft Excel file(textE_to_affy.csv) which contains the Microarray Expression Values collected from the Illumina Microarray experiment. These collected intensity values need to be normalized(Rank Invariant Normalization) by using the R

Hi all, I encountered a problem when trying to read in an Illumina chip annotation file. The offending file is large, so I zipped it up and posted it at http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/tmp/ProbeInfo_Expression.txt.bz2 Executing this: annot = read.table(bzfile("ProbeInfo_Expression.txt.bz2"), comment.char="", sep =

so much for the markdown listserve grapevine... it ends up that there has been a markdown-savvy display-in-real-time app for a couple months now, by the name of "macchiato", coded by a college kid. > http://getmacchiato.com > http://kswizz.com/post/8624456381/macchiato > http://mac.onedayoneapp.com/macchiato/ > http://shawnblanc.net/2011/08/macchiato/ >

I have a boxplot of Production run rates per 10 minute intervals and I would like to color code them by the average (i.e. >15ppm = green, <9ppm = red, everything else yellow). Is there a way to do this? http://r.789695.n4.nabble.com/file/n4289381/RunRateBoxWhisker.png -- View this message in context: http://r.789695.n4.nabble.com/Add-color-to-Boxplot-by-value-tp4289381p4289381.html Sent

This is a continuation of my previous posts about improving write perf when trapping millions of small writes to a gluster filesystem. I was able to improve write perf by ~30x by running STDOUT thru gzip to consolidate and reduce the output stream. Today, another similar problem, having to do with yet another bioinformatics program (which these days typically handle the 'short reads' that

i m searching on net,material related to R, whenever i get ppt presentation of some topic ,i found it in speical format white backgroud & blue bars,having links for further topics see link 1) https://www.rmetrics.org/files/Meielisalp2007/Presentations/Pfaff.pdf 2)http://grapevine.com.au/~yanchang/docs/Time-Series-Mining-slides.pdf If this is format,how can i made it,if i want to give my R

Hey All, I've been using Asterisk for a couple years now, but have always had some unsolvable audio problems. I get audio stuttering and popping quite often. Even if I have just one call up! The server is a Dual Duo-Core 3.0ghz Xeon Processor PC with 4 GB or ram. It just seems to me that this should NOT be happening. The server resources are nearly 98% idle. I've tried using

Hi, Last year our systems group tried to install R on an IBM p5-570 machine (16 nodes, 256 GB shared RAM), running AIX 5.3. They ran into all sorts of difficulties and finally gave up. I am interested in trying again (and working with an IBM support group if necessary), but before embarking on this odyssey I was wondering if anyone on this list has ever successfully run R on a similar

This is somewhat a summary/continuation of an R bug report: (https://bugs.r-project.org/bugzilla3/show_bug.cgi?id=14645) Illumina's cluster definition files (*.egt) are one of the proprietary and undocumented file formats used by their GenomeStudio line of products for genomic studies. snpMatrix 1.17.0.7 onwards (http://sourceforge.net/projects/outmodedbonsai/files/snpMatrix%20next/)

The beta version of turnpike 6 is out. I'm using it here, but under win4lin. A big point of the new version is that it uses windows explorer, and I had heard on the grapevine that it was therefore going to be a problem proggie for wine. I've tried running the v6 'connect' program under wine - that works fine (downloads a new newsgroup list, gets me an e-mail - when WILL I be

In my experience software compiled for RHEL "just work" with Centos and I don't remember any case where it didn't. I have however heard whisperings on a grapevine that RH may want to try and make future versions of Centos slightly incompatible with RHEL but these are probably just whisperings. If you software vendor will not support Centos as RHEL then they probably need a good

Some background... We use AMI and AsyncAGI to be able to receive events about calls (and other Asterisk details) and control it from our application. Works great and have about 100 sites (some newer, some older) without issues. I was notified this morning about a customer who had something strange happen and I can't explain it. Asterisk 16.23.0 and PJSIP. Call comes into Asterisk. Asterisk

Dear Bioc and R List Users, I am having trouble analysing illumine data generated from BeadScan. I have .idat files and JPEG images. I realise that i need bead-level summary data to be able to begin quality control followed by normalization. Is there a way i can read .idat files for expression analysis or do i need to go back to BeadScan and generate .txt files/tiff files ? Appreciate any help