similar to: Add color to Boxplot by value

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:

Hey So sorry to be a total newbie, but i'm just finding my feet with R. I heard on the grapevine i could recreate a scanned microarray image, or at least get a good graphic of it from a just a data file. I have .txt files for illumina beadarrays but no images cos the service we used didn't send them. The 'beadarray' package seems to require TIFFs to get the graphic output. Does

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:

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, 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

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 =

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

Hi, I'm stumped. How can I do ftell and fseek in R? (Where ftell gives the position in the file and fseek points the file pointer to a given position.) Thanks, Pauline -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.- r-help mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html Send "info", "help", or

Hi, I am trying create a grouped barplot (with beside=T) and would like to plot the bar groups, not the individual bars, with a variable width. To give an example, I would like all bars in the first group to have the default size of 1, all bars in the second group 2, in the third 3, etc. If I use width=c(1,2,3,..), it applies these settings to individual bars, e.g. the first bar in the first

Issue: Connecting to a computer in a network. I would like to connect to a file on a computer on my internal network that has a different password. I have tried download.file and read.csv to no avail. When use this link in explorer it will prompt me for a username/password: file://hs9999-907/D$/protein%20Maintenance%20Logs/123.txt Then it lets me through. I cannot get any R traction on where I

Hello All I have a very long vector of unique predictor values and 6 significant digits setting for the smooth.spline rounds them off. Is there any way of increasing the significant digits withour recompiling a lot if code (simple editing and tham sourcing of "smooth.spline.r" function does not work, probably due to presence of Fortan functional calls)? Thank you very much in advance