User: Ludwig Geistlinger

Reputation:
40
Status:
New User
Location:
Germany
Last seen:
2 months, 1 week ago
Joined:
7 years, 9 months ago
Email:
L*****************@bio.ifi.lmu.de

Posts by Ludwig Geistlinger

<prev • 8 results • page 1 of 1 • next >
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Answer: A: RNA-seq data type gets error when using sbea
... Hi Ai Chen, (1) perhaps you want to change the title of your post to something more precise such as: "Error when using EnrichmentBrowser's sbea function with RNA-seq data" (2) You maybe by accident also created another post https://support.bioconductor.org/p/90490/ reporting on the same error t ...
written 11 months ago by Ludwig Geistlinger40
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News: Announcing the EnrichmentBrowser 2.0
... Dear Bioconductors, I am delighted to announce a major re-release of the EnrichmentBrowser package in line with its recent publication: Geistlinger L, Csaba G, Zimmer R. Bio ...
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Answer: A: Gviz: add/change bands in ideogram
... that works. great! thank you! ...
written 3.0 years ago by Ludwig Geistlinger40
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Answer: A: Gviz: add/change bands in ideogram
... Hi Florian, BTW: great work on the Gviz package, I found it to be the best among its kind and recommend it also to others! Your suggestion to fill gaps in the bands df with gneg bands indeed resolved the error, however now the plot looks weird. Please find the dataframe below. I used the code as ...
written 3.0 years ago by Ludwig Geistlinger40
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Gviz: add/change bands in ideogram
... Hi,   As other users encountered as well: There is no information available on cytobands for my organism. Specifically, I'm plotting chr12 of bosTau6 giving me an empty ideogram, which is fine.   gen <- "bosTau6" chr <- "chr12" start <- 71959908 end <- 77206892 ideoTrack <- ...
gviz written 3.0 years ago by Ludwig Geistlinger40
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Answer: A: Differential gene expression of Microarray data
... Hi, you can use the 'volcano' function from the EnrichmentBrowser package in case you have your data in an ExpressionSet. Otherwise you can just use these lines: I assume <fcs> to be a vector of log2 fold changes and <ps> a vector of e.g. t-test derived p-values: plot(x=fcs,         ...
written 3.1 years ago by Ludwig Geistlinger40 • updated 3.1 years ago by Gordon Smyth32k
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KEGGgraph: retrieveKGML error (due to wrong ftp path)
... Dear BioC developers, as I try to use the retrieveKGML function of the KEGGgraph package, I end up with the following error: ------ retrieveKGML(pathwayid='00010', organism='cel', destfile="/home/cbio/ludwig/test.txt", method="wget") --17:06:46-- ftp://ftp.genome.jp/pub/kegg/xml/organisms/cel/cel ...
kegggraph written 7.7 years ago by Ludwig Geistlinger40 • updated 7.7 years ago by Cristobal Fresno Rodríguez350
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KEGGSOAP, hgu95av2.db: limited functionality
... Dear BioC developers, I intend to map gene expression data on KEGG pathways. In more detail, I performed a DE analysis on gene expression data from a hgu95av2 chip and want to color particular genes in corresponding pathways. I found out that the KEGGSOAP package already implemented an awesome acce ...
pathways hgu95av2 probe keggsoap written 7.8 years ago by Ludwig Geistlinger40 • updated 7.8 years ago by Marc Carlson7.2k

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