User: Michael Dondrup

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Posts by Michael Dondrup

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Comment: C: agi4x44preprocess
... Hi, looks like you just got a '.' too much in the header line in your targets file: 'File.Name' vs 'FileName'. Best Am 28.10.2009 um 20:17 schrieb Neel Aluru: > Hi Tobias, > > Thanks for your help. I tried your suggestion and it keeps giving me > a new error message. Here are the deta ...
written 8.1 years ago by Michael Dondrup140
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Comment: C: Most stable gene pairs in array experiment
... Hi, one can of course compute a lot of things the question is if that makes sense. The term 'stability' is as far as i know not well defined in the statistical sense, however there is a definition of numerical stability for algorithms. http://en.wikipedia.org/wiki/Numerical_stability Therefor, use ...
written 8.1 years ago by Michael Dondrup140
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Comment: C: Most stable gene pairs in array experiment
... Hi, you can try something like this or use two for loops: > apply (mygenes, 1 , function(row) { apply (mygenes, 1, function(x) { var(row-x) } ) } ) geneA geneB geneC geneD geneE geneA 0.00000 0.04108 0.06397 0.12217 0.08233 geneB 0.04108 0.00000 0.15543 0.12807 0.09365 gen ...
written 8.1 years ago by Michael Dondrup140
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Comment: C: regarding web interface to R coding
... The choice of the appropriate language to build a user interface depends on - your skills in the programming languages - your requirements, e.g. full blown AJAX web 2.0 with virtual desktop in the browser behavior vs. single CGI page - availability of libraries for user-interfaces meeting these req ...
written 8.2 years ago by Michael Dondrup140
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Answer: A: regarding web interface to R coding
... Hi Ankhee, depends mainly on your favorite host language I think. Among other suggestions (RPy), I think one of the most commonly used solution is Java and the rJava package. That can be installed from CRAN. That contains JRI so you can run R code from Java (and vice versa), I know some people that ...
written 8.2 years ago by Michael Dondrup140
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Answer: A: sequence-motif visuazation (motifs found with DNAString)
... Hi, maybe you can try the seqLogo package seqLogo Sequence logos for DNA sequence alignments seqLogo takes the position weight matrix of a DNA sequence motif and plots the corresponding sequence logo as introduced by Schneider and Stephens (1990). that could visualize the motif part when given a P ...
written 8.2 years ago by Michael Dondrup140
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Answer: A: Merging RandData object with names on the IRanges part
... Hi Ulrike, I think you can use function c(). you then can get the IRanges names preserved in your examples: > ranges(c(t1,t2))[[3]] IRanges object: start end width names [1] 7828367 7828402 36 a [2] 7828552 7828587 36 b Michael Am 20.08.2009 um 17:03 schrieb Ulrike G ...
written 8.3 years ago by Michael Dondrup140
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Reading GFF files into R and GenomeGraphs
... Hi, it took a while to figure out how to read genome annotation files with and without rtracklayer, thanks Michael, and also how to plot bacterial chromosomes using the GenomeGraphs package. I think, this information can be useful for others, so I made a tiny howto. I think some of this could also b ...
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Answer: A: about the annotate the new genome for geneplotter/genegraph
... Dear Zhuo-Cheng, I am currently having a similar problem using the GenomeGraphs package. It seems that as long as you are doing mainstream, like human, mouse, things are fine, very easy to work with these packages, but as soon as you try something that is a little more uncommon, you are immediately ...
written 8.3 years ago by Michael Dondrup140
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Reading GFF files into R and GenomeGraphs
... Dear BioC list, I'm trying to use the package GenomeGraphs to visualise custom genome data (genome not in public databases). In the corresponding publication to genomegraphs (Durinck et al. BMC Bioinformatics, 2009 ) I found the partial clue: "... genomic annotation encoded in GFF files can be easi ...
annotation genomegraphs written 8.3 years ago by Michael Dondrup140 • updated 8.3 years ago by Michael Lawrence620

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Popular Question 8.1 years ago, created a question with more than 1,000 views. For Reading GFF files into R and GenomeGraphs

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