User: Forst, Christian

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Posts by Forst, Christian

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Comment: C: Directed MST (Edmond's Algorithm)
... That may work - thanks. ________________________________________ From: bioconductor-bounces@r-project.org [bioconductor- bounces@r-project.org] on behalf of Vincent Carey [stvjc@channing.harvard.edu] Sent: Tuesday, October 22, 2013 13:31 To: Paul Shannon Cc: Steve Lianoglou; bioconductor at r-proje ...
written 5.6 years ago by Forst, Christian90
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Comment: C: Directed MST (Edmond's Algorithm)
... Thank you. Unfortunately Prim's algorithm only works for undirected graphs (AFAIK). Edmond's algorithm would be able to utilize directionality. Christian ________________________________________ From: mailinglist.honeypot@gmail.com [mailinglist.honeypot@gmail.com] on behalf of Steve Lianoglou [lia ...
written 5.6 years ago by Forst, Christian90
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Directed MST (Edmond's Algorithm)
... I am looking for an implementation of Edmond's (or better) algorithm to calculated a directed minimum spanning tree from a directed graph. I found the edmondsOptimumBranching() function in the RBGL package but I am struggling in getting my graphs (from edge-lists) in the right format. I would guess ...
go graph rbgl written 5.6 years ago by Forst, Christian90 • updated 5.6 years ago by Steve Lianoglou12k
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MetaboLights, wiff-files
... Is there a BioC-package to access data from EMBL-EBI's MetaboLights database (including wiff-files)? A search at bioconductor.org didn't yield anything. Christian ...
written 5.9 years ago by Forst, Christian90
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gage: essGene()
... Can gage::essGene() use pre-ranked expression data or does it require a matrix so that two distinct groups can be compared? ?essGene: exprs in essGene should be "an expression matrix or matrix-like data structure, with genes as rows and samples as columns." Same is true, for example, for the funct ...
written 6.3 years ago by Forst, Christian90
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Comment: C: ExpressionSet Time-series correlation stuff
... Yes, using the transpose and supplying two matrices to cor() is doing the trick. Thanks again Chris ________________________________________ From: James W. MacDonald [jmacdon@uw.edu] Sent: Tuesday, January 22, 2013 17:02 To: Forst, Christian Cc: bioconductor at r-project.org Subject: Re: [BioC] Exp ...
written 6.3 years ago by Forst, Christian90
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Comment: C: ExpressionSet Time-series correlation stuff
... Thanks but it doesn't really do what I want. First I still need to do sp <- cor(exprs(es[,ts])) instead of sp <- cor(es[,ts]) Otherwise I get Error in cor(es[,ts]) : supply both 'x' and 'y' or a matrix-like 'x' Then, sp is a square matrix over ts and not over the time-correlated genes whi ...
written 6.3 years ago by Forst, Christian90
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ExpressionSet Time-series correlation stuff
... Is there an easier way to do time-series correlation between genes of an ExpressionSet other than using for-loops and cor()? especially if I want to play with the particular time-series? And I am not really happy with the packages I found so far: bioDist, qpgraph, qvalue I have: es...ExpressionSet ...
biodist written 6.3 years ago by Forst, Christian90 • updated 6.3 years ago by James W. MacDonald50k
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Basic ExpressionSet problems
... I have some basic problems with the ExpressionSet class of Bioconductor (as beginning user). For example, I do the following. gse40012 <- getGEO("GSE40012") es40012 <- gse40012[[1]] a40012<-addGeneInfo(es40012, annotationLibrary = "illuminaHumanv3") Now I want to export the now available a ...
annotation written 6.4 years ago by Forst, Christian90 • updated 6.4 years ago by Sean Davis21k

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