search for: illumina

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/) contains codes for reading that file...

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, evaluate it and write it back into a t...

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 anone know of a way/a package i can use to rebuild the image? Cheers! -- View this message in context: http://r.789695.n4.nabble.com/Com...

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 mess...

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-cal...

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=&...

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 function "normalize.AffyBatch.invariantset()". Since the normalize.AffyBatch.invariantset() method requires the input argument to be an AffyBatch Object, I used the...

...t of the majority of sequencing hardware, each read being 30-150 characters, with some metadata typically in an ASCII file containing millions of such entries). Reading them doesn't seem to be a problem (at least on our systems) but writing them is quite awful.. The program is called 'art_illumina' from the Broad Inst's 'ALLPATHS' suite and it generates an artificial Illumina data set from an input genome. In this case about 5GB of the type of data described above. Like before, the gluster process goes to >100% and the program itself slows to ~20-30% of a CPU. In this ca...

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 Th...

...g. the first bar in the first group has size 1, the second bar size 2, etc. which is not what I want. Is there are way to accomplish this? Sorry if this has been discussed before, I searched on the web and the archive of this list but could not find anything. Regards, Ole Schulz-Trieglaff --- Illumina Cambridge Ltd. UK Computational Biology Group United Kingdom

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

...ization. The applicant must be able to demonstrate excellence in the following areas: Strong programming experience in C/C++; Strong data analysis experience using R/Bioconductor, Java/Python; Unix shell programming; Experience in the analysis of high-??throughput sequencing data (preferably Solexa/Illumina and 454 sequence data); Experience in genome structural variation detection; Familiarity with Galaxy or other pipeline building system; Experience in parallel computing using clusters; The applicant should work well in a group as well as be able to move forward independently. Good documentation ski...

...es and Responsibilities: We have an opening in the pharmacogenomics group within the translational science department. We are looking for a highly motivated computational biologist/bioinformatician with experience in large-scale sequence analysis of data generated by technologies such as Roche 454, Illumina, or AB SOLiD. Additional background in the following is required: statistical analysis, predictive modeling, and algorithm development to support research into the pathways and other biological mechanisms underlying drug response. The candidate should also have demonstrated proficiency in the analy...

...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 Protectio...

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