User: Ludwig Geistlinger
Ludwig Geistlinger • 50
- Reputation:
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- USA/NYC/CUNY
- Last seen:
- 2 months, 3 weeks ago
- Joined:
- 9 years, 8 months ago
- Email:
- l*****************@sph.cuny.edu
Posts by Ludwig Geistlinger
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... GSEA works on the full gene vector, testing whether genes of a gene set (here: a KEGG pathway) accumulate at the top or bottom of the full gene vector ordered by direction and magnitude of expression change.
If you are interested only in genes of significant expression change (here: abs(log2FC) > ...
written 3 months ago by
Ludwig Geistlinger • 50
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... Thanks a lot for this comprehensive answer and these great suggestions.
Although there are scenarios where a CNV can affect gene expression on a genome-wide
scale (eg by modulating the expression of a coinciding transcription factor, which
in turn regulates distal genes), you rarely have the power t ...
written 13 months ago by
Ludwig Geistlinger • 50
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... Dear edgeR-Team,
I have around 200 samples for which I have
1) CNV data, ie. a matrix X (regions x samples) in which a cell is either 2 (normal diploid), 0/1 (loss), or 3/4/5/... (gain),
2) RNA-seq data, ie. a matrix Y (genes x samples) storing the raw RNA-seq read counts.
Now I want to find for ...
written 13 months ago by
Ludwig Geistlinger • 50
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... Not sure whether this is what you are aiming for with rtracklayer::liftOver, but I assume general consistency with the UCSC online liftOver (https://genome.ucsc.edu/cgi-bin/hgLiftOver) to be a desired feature for many users.
I can think of several good use cases, but to give you a specific one:
Co ...
written 16 months ago by
Ludwig Geistlinger • 50
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... 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 2.8 years ago by
Ludwig Geistlinger • 50
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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 ...
written 3.7 years ago by
Ludwig Geistlinger • 50
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... that works. great! thank you!
...
written 4.9 years ago by
Ludwig Geistlinger • 50
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... 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 4.9 years ago by
Ludwig Geistlinger • 50
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... 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 <- ...
written 4.9 years ago by
Ludwig Geistlinger • 50
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... 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 5.0 years ago by
Ludwig Geistlinger • 50
• updated
5.0 years ago by
Gordon Smyth ♦ 38k
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