User: Ivanek, Robert

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7 years, 5 months ago
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r************@fmi.ch

Posts by Ivanek, Robert

<prev • 10 results • page 1 of 1 • next >
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Answer: A: shift function (GenomicRanges, IRanges), issue with negative start values and ci
... Hi Herv?, On 01/23/2012 01:04 AM, Hervé Pagès wrote: > Hi Robert, > > Sorry that this completely went off my radar but this week someone > kindly sent me a reminder. > > So after re-reading your email I agree that shift() should behave > consistently on both ends of the chromos ...
written 7.4 years ago by Ivanek, Robert100
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Comment: C: shift function (GenomicRanges, IRanges), issue with negative start values and ci
... Hi Michael, is there any plan to fixed these issues? Best Regards Robert On 09/01/2011 03:37 PM, Michael Lawrence wrote: > Nevermind, I misunderstood what you were trying to do. > > On Thu, Sep 1, 2011 at 6:36 AM, Michael Lawrence > wrote: > > As a sort of side-comment, yo ...
written 7.8 years ago by Ivanek, Robert100
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shift function (GenomicRanges, IRanges), issue with negative start values and circular DNA
... ## ################################################################### ########## ## library("GenomicRanges") ## Loading required package: IRanges ## Attaching package: ‘IRanges’ ## The following object(s) are masked from ‘package:base’: ## cbind, eval, intersect, Map, mapply, order, pas ...
written 7.8 years ago by Ivanek, Robert100 • updated 7.8 years ago by Michael Lawrence11k
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pdInfoBuilder -- MOUSEDIVm520650
... Dear BioC list, I would like to create the annotation package for Affymetrix Mouse Diversity Array (MOUSEDIVm520650) and run CNV analysis on these arrays. However I am missing three files, which are required to successfully build the annotation package and run the analysis. splineParamFile crlmmI ...
annotation pdinfobuilder crlmm written 9.1 years ago by Ivanek, Robert100 • updated 9.1 years ago by James W. MacDonald50k
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Mouse diversity array --building the required files for aroma.affymetrix UGP, UFL
... Dear Sir or Madam, I would like to analyse the copy number variation data from Affymetrix Mouse Diversity Array. I have not found any information on your website about this particular array. I have tried to build the annotation files which are required by aroma but without success. I have few quest ...
cdf written 9.1 years ago by Ivanek, Robert100
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Comment: C: snapCGH, runBioHMM, Error: segfault from C stack overflow
... Hi Seth, I tried it with a new version of R and BioConductor but I am still getting the same error. Any ideas? Robert R> SegInfo.BioHMM <- runBioHMM(MA.cgh2) sample is 1 Chromosomes: 1 2 Error: segfault from C stack overflow R> class(MA.cgh2) [1] "SegList" attr(,"package") [1] "sn ...
written 9.3 years ago by Ivanek, Robert100
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Comment: C: snapCGH, runBioHMM, Error: segfault from C stack overflow
... Hi Seth, OK, I will try it with devel version of R. I thought I copied the information to my previous email but here it is once again: ###################################################################### ########## R> SegInfo.BioHMM <- runBioHMM(MA.cgh2) sample is 1 Chromosomes: 1 2 ...
written 9.3 years ago by Ivanek, Robert100
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snapCGH, runBioHMM, Error: segfault from C stack overflow
... Dear John, BioC-community, I tried to run the runBioHMM function on my data (Nimblegen HD 2.1 Arrays), however I am always getting the error: "Error: segfault from C stack overflow". What is the reason for that error? Are the data too big? I tried to split the array according the chromosomes but i ...
snapcgh written 9.3 years ago by Ivanek, Robert100 • updated 9.3 years ago by Seth Falcon150
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Answer: A: biomaRt- incorrect number of transcripts
... Dear Steffen, I originally used only unique transcripts. I guess that this is not the reason for different number of transcripts. As you can see below in the original mail: the incorrect number of transcripts is obtained via biomaRt package only for some chromosomes and only if the filter is set to ...
written 9.6 years ago by Ivanek, Robert100
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biomaRt- incorrect number of transcripts
... Dear mailing list, I have recently observed a discrepancies in genome annotation obtained via R package biomaRt. I wanted to download all ensembl transcripts from the entire mouse genome (chromosome 1:19, X, Y MT only). When I set the filter based on chromosome names I retrieved ~36000 transcript, ...
annotation biomart written 9.7 years ago by Ivanek, Robert100

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