search for: illuminae

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/)

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

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,

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

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

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 =

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

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've got a microarray dataset (Illumina) coming from a blood assay with a case-control factor of interest. I also have several other covariates (gender, weight, etc...). I know that the experimental design is highly unbalanced with respect to Gender: female male control 12 7 case 7 17 Therefore, if there is a Gender effect, then it really

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

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

Please do NOT contact me for this post. Please see below for contact details. The company offers solutions for the secure storage and analysis of patient genome sequence information to enable its effective, confidential application to personalized healthcare. The jobholder will be involved in clinical next generation sequence (NGS) data analysis pipeline development. The candidates will be

Bioinformatics Scientist position in Maryland Description Title: Bioinformatics Scientist I/II - Translational Science Location - Gaithersburg, MD Contact: higgsb at medimmune.com ** Please do not send a CV if you do not have most of the qualifications listed below ** Local candidates preferred Major Duties and Responsibilities: We have an opening in the pharmacogenomics group within the

...seases Larry Simpson Howard Hughes Medical Institute/UCLA. USA Jose Stoute, US Army Medical Research Command. USA John H Adams, Center for Tropical Disease Research & Training. University of Notre Dame, USA Bioinformatics Elia Stupka, Temasek Life Sciences Laboratory. Singapore Mark Wilkinson, Illuminae Media, Canada Akihiko Konagaya, RIKEN Genomic Sciences Center, Japan David Sankoff, Department of Mathematics and Statistics. University of Ottawa. Canada Transcriptional Analysis Bruce Aronow, Cincinnati Childrens Hospital Medical Center. USA Bioethics and Intellectual Property Rights Protection...

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

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

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