similar to: Error in sort(abs(diff(genomdat)))[1:n.keep] : only 0's may be mixed with negative subscripts

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

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 =

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

We're running rsync 2.5.7 on a Windows2000 server, in combination with cygwin/ssh. The server who receives the data is a Linux server. The amount of data from the Windows server is about 100 Gb. Represented by 532.000 files of different nature. Mostly doc, ppt and xls files. It takes about 2 hours to create only the file list. Is the amount of data/files to big, should I segmentate the

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 R users and developers After upgrading to Windows XP and R 1.9.1 and 2.0, I retried to execute plot.baysian() to a data set that I had used previously to plot with no problem in win2000 R1.8. The error I get is: Error in points(Mbar[-index], lods[-index], pch = ".") : only 0's may mix with negative subscripts Thanx in advance Dino P.S. I allready sent this message

Hi all, I have just started using RMark to analyse capture-recapture data. I am trying to analyse a simulated data set using the Robust Design (two primary periods with three secondary sessions in each) to estimate apparent survival. On specifying the time intervals (that tell R about the primary and secondary sampling sessions), this is the error I get: > time.int <- c(0,0,1,0,0) >

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

On Jan 19, 2009, at 7:55 AM, Andrew Haley wrote: > This is x86_64. I have a problem where an absolute memory load > The current LLVM trunk does not have this bug. This seems quite a > nasty > bug; is there any chance of a bug-fix release for LLVM 2.4, or > should I > just use LLVM trunk until LLVM 2.5 ? Hi Andrew, As others have pointed out, using a global and

I add a function abs64 to support abs for 64 bit integer -- 此致 礼 罗勇刚 Yours sincerely, Yonggang Luo -------------- next part -------------- A non-text attachment was scrubbed... Name: llvmabsfault.patch Type: application/octet-stream Size: 800 bytes Desc: not available URL: <http://lists.llvm.org/pipermail/llvm-dev/attachments/20090809/0d1aa27d/attachment.obj>

It's the same as PR#2993, fixed yesterday in R-patched & R-devel On Fri, 30 May 2003 rossini@blindglobe.net wrote: > > Something like the following should be done for power.t.test to make > sure that it doesn't try to evaluate abs(NULL), which results in an > error. That's a backwards patch, I presume, or you revert the fix. > --- rossini.power.t.test.R

Hello list reader, I am trying to form some constraints for an optimization I am working on. I think I have understand the use of the constraints in matrix form. I use them like: constr_mat<- -diag(2) constr_vec<- rep(-0.05,2) constr_mat<- rbind(constr_mat, diag(2)) constr_vec<- c(constr_vec, rep(-1, 2)) To get parameters in the interval [-1, 0.05]. (And this works so far) Now I

I might be wrong, but didn't the following work before R v1.4.x? R --vanilla > df <- data.frame(-10:10) > abs(df) Error in abs(df) : non-numeric argument to function I have tried this on both Rv1.4.1 on WinMe and Rv1.4.0 on Solaris 8. I regexp searched bugs.r-project.org on "abs" but I found nothing about this. I can't see why abs(df) shouldn't work when sqrt(df),

I might be wrong, but didn't the following work before R v1.4.x? R --vanilla > df <- data.frame(-10:10) > abs(df) Error in abs(df) : non-numeric argument to function I have tried this on both Rv1.4.1 on WinMe and Rv1.4.0 on Solaris 8. I regexp searched bugs.r-project.org on "abs" but I found nothing about this. I can't see why abs(df) shouldn't work when sqrt(df),

On Jan 20, 2009, at 2:10 AM, Andrew Haley wrote: > Chris Lattner wrote: >> On Jan 19, 2009, at 7:55 AM, Andrew Haley wrote: >> >>> This is x86_64. I have a problem where an absolute memory load >>> The current LLVM trunk does not have this bug. This seems quite a >>> nasty >>> bug; is there any chance of a bug-fix release for LLVM 2.4, or