## User: Forst, Christian

Forst, Christian •

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- 6 years, 4 months ago
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- c**************@mssm.edu

#### 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, Christian •

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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, Christian •

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... 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 ...

written 5.6 years ago by
Forst, Christian •

**90**• updated 5.6 years ago by Steve Lianoglou ♦**12k**0

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... 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, Christian •

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... 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, Christian •

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... 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, Christian •

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... 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, Christian •

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... 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 ...

written 6.3 years ago by
Forst, Christian •

**90**• updated 6.3 years ago by James W. MacDonald ♦**50k**0

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... 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 ...

written 6.4 years ago by
Forst, Christian •

**90**• updated 6.4 years ago by Sean Davis ♦**21k**#### Latest awards to Forst, Christian

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