User: arne.mueller@novartis.com

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Posts by arne.mueller@novartis.com

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Comment: C: Problem installing BSgenome.Hsapiens.UCSC.hg19
... Hi - I had a similar problem when tray to load BSgenome packages. The problem was some entry in the LD_LIBRARY_PATH environment variable (Linux). I reset my LD_LIBRARY_PATH to the bare minimum and this solved the problem. Seems some package (probably) loaded the wrong version of a share library. ...
written 2.9 years ago by arne.mueller@novartis.com200
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Matrix package bug?
... Hello, I'm using R 3.0.0 and trying to construct a fairly large sparse matrix with the Matrix package (40,567 columns and 64,323 rows ) and get the following error: Error in asMethod(object) : negative length vectors are not allowed Could this be an overflow problem, I thought R 3 would support l ...
written 5.0 years ago by arne.mueller@novartis.com200 • updated 5.0 years ago by Martin Morgan ♦♦ 22k
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Limma removeBatchEffect
... Hello, I've a question regarding the removeBatchEffect function in limma. I basically have a model expression_signal ~ organ + species + organ:species in which species can be considered a batch effect (I expect differences between species due to mainly due to array platform differences). I'd like t ...
limma written 5.0 years ago by arne.mueller@novartis.com200 • updated 5.0 years ago by James W. MacDonald47k
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GRanges performance issue
... Hello, I realized there's a massive performance difference to subset Granges objects by name compared to the Granges subset method. Example: > length(mm9.tiled) [1] 5309835 > n = names(mm9.tiled) > rn = sample(n, 1000) > system.time(tmp <- subset(mm9.tiled, names(mm9.tiled) %in% rn ...
written 7.1 years ago by arne.mueller@novartis.com200 • updated 7.1 years ago by Hervé Pagès ♦♦ 13k
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GRanges nearest problem
... Hello, I've come across a problem in GRanges nearest, if subject of the nearest call contains strand information (+/-) and the query does not (*), the method takes a long time to run and raises warnings: mm9.pro.gr and mm9.2ktiles.gr are both Granges objects. > strand(mm9.pro.gr) = "-" > s ...
written 7.3 years ago by arne.mueller@novartis.com200 • updated 7.3 years ago by Valerie Obenchain ♦♦ 6.5k
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Comment: C: multicore and GRangesList
... Hello, thanks, all for your reply. The doMC works fine for me. Nevertheless, there seems to be some overhead since at the beginning and the end of the loop. The initial R-process doesn't fork immediately and when all child processes are finished the parent still processes for quite some time befor ...
written 7.6 years ago by arne.mueller@novartis.com200
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multicore and GRangesList
... Dear All, Has anybody experience using the multicore package with GRangesLists from the GenomicRanges package? I can't get it working ..., here's an example: > a = GRanges(seqnames="A", ranges=IRanges(start=1:3, width=5)) > b = GRanges(seqnames="A", ranges=IRanges(start=c(10,20,30), width=5) ...
genomicranges written 7.6 years ago by arne.mueller@novartis.com200 • updated 7.6 years ago by Martin Morgan ♦♦ 22k
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affymetrix annotation
... Hi Jim, sorry for the very late reply, and thanks a lot for your detailed answer. This makes perfectly sense to me! best regards, arne "James W. MacDonald" 12/21/2010 04:30 PM To arne.mueller@novartis.com cc bioconductor@stat.math.ethz.ch Subject Re: [BioC] affymetrix annotation H ...
annotation mouse4302 affy written 7.6 years ago by arne.mueller@novartis.com200
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Answer: A: Idea that needs feedback
... Hi, in principle this sounds good, but it seems there's much overlap with the bioconductor web-site that already offers, packages, workflows, documentation, tutorials and hands-on hints and discussion (mailing list) ... In my experience many packages are as abstract as possible (IRanges and off-sp ...
written 7.6 years ago by arne.mueller@novartis.com200
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Comment: C: affymetrix annotation
... Hello, thanks Jim for your reply. The org.Mm.eg.db::org.Mm.egSYMBOL has the gene symbol for the probeset of interest, it's just mouse4302 that's missing it. I've just checked in an older netffx annotation files (older than 2007, 2009, and the current one from 2010). The probeset was annotated alre ...
written 7.6 years ago by arne.mueller@novartis.com200

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