Moderator: Wolfgang Huber

gravatar for Wolfgang Huber
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Location:
EMBL European Molecular Biology Laboratory
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http://www.embl.de/res...
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14 years, 7 months ago
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Posts by Wolfgang Huber

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Comment: C: Why does rlog and vst use normalized counts?
... Re peculiarities of single cell data: "...you often have genes which are mostly 0's but then highly expressed in a minority of cells": these are likely not really highly expressed genes, but rather, low expressed ones that just happen to have gotten highly (PCR)-amplified in a few cells. That al ...
written 25 days ago by Wolfgang Huber12k
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Answer: A: Best practices for converting adj matrix -> graphNEL
... Dear Bryon I am not sure there is "the intended method". Most of the code in this package is >10 years old, and it was contributed by several authors at the time. So, contributions and patches from you will also be welcome. Some observations that might be useful: as(adj, "graphNEL") with adj ...
written 4 weeks ago by Wolfgang Huber12k
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Job: PhD-level staff position in computational modelling and quantitative biology at EMBL
... Computational Biologist (mathematical modelling) Location: Heidelberg, Germany Staff Category: Staff member Contract Duration: 3 years Grading: 6, 7 or 8; depending on qualification and experience Closing Date: 18 January 2017 ...
modelling job exciting written 4 weeks ago by Wolfgang Huber12k
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Answer: A: how to change color of points log2foldchange>1
... Use this xs <- x[x$baseMean>1, ] plotMA(xs, col = ifelse(xs$log2FoldChange>1, "red", "gray")) ...
written 4 weeks ago by Wolfgang Huber12k
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Answer: A: Bug in cleanUpPhenoData
... Dear Flo Thank you for the report and precise dissection of the problem.  This should be fixed in arrayQualityMetrics version 3.31.2 in the devel branch. (Thanks to Andrzej Oles for testing and completing my fixes!) Wolfgang ...
written 6 weeks ago by Wolfgang Huber12k
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Answer: A: Fastest way to get the distances between pairs of graph nodes
... How about dijkstra.sp in the RBGL package? ...
written 6 weeks ago by Wolfgang Huber12k
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Comment: C: Weighted matrix from igraph to graphNEL
... Can you please provide a self-contained code example, and your sessionInfo?   ...
written 7 weeks ago by Wolfgang Huber12k
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Comment: C: How to avoid repeated overlap pair for GRanges object in grid?
... And  combn(N, 2) is handy in such cases. ...
written 9 weeks ago by Wolfgang Huber12k
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ExperimentHub()[["EH359"]] has character expression values
... I am not sure what the right protocol is for reporting bugs in ExperimentHub, but here we go. It appears that the dataset ExperimentHub()[["EH359"]] (apparently a.k.a. curatedMetagenomicData::ZellerG_2014.marker_abundance) is an ExpressionSet whose exprs is a matrix of characters. The matrix can be ...
experimenthub curatedmetagenomicdata written 10 weeks ago by Wolfgang Huber12k • updated 6 weeks ago by Lucas Schiffer50
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Answer: A: Bioconductor packages for machine learning with RNAseq
... Sara perhaps you are referring to characteristics of RNA-Seq data that make it necessary to "preprocess" the data before applying regular ML methods: normalisation for library size and transformation to make the data less skewed and less heteroskedastic. Have a look at the variance stabilizing tran ...
written 10 weeks ago by Wolfgang Huber12k

Latest awards to Wolfgang Huber

Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Deseq2 error estimating size factors -- zeros in count matrix
Scholar 10 months ago, created an answer that has been accepted. For A: arrayQualityMetrics error: Error: Unknown parameters: cex.axis
Scholar 12 months ago, created an answer that has been accepted. For A: arrayQualityMetrics error: Error: Unknown parameters: cex.axis
Scholar 13 months ago, created an answer that has been accepted. For A: plotMA for unshrunken LFC in deseq2
Scholar 18 months ago, created an answer that has been accepted. For A: rounding issues using the VSN package
Scholar 18 months ago, created an answer that has been accepted. For A: rounding issues using the VSN package
Supporter 20 months ago, voted at least 25 times.
Scholar 2.1 years ago, created an answer that has been accepted. For A: arrayQualityMetrics: "All SVG style attribute must have length 1" and other erro
Centurion 2.3 years ago, created 100 posts.
Oracle 7.5 years ago, created more than 1,000 posts (questions + answers + comments).

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