Moderator: Wolfgang Huber
Wolfgang Huber ♦ 13k
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Posts by Wolfgang Huber
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... I don't know how to get this to work with GNU binutils. The authoritative source on recommended build configuration is probably https://www.bioconductor.org/checkResults/release/bioc-LATEST/merida1-NodeInfo.html .
On my notebook with MacOS Mojave, R itself and the lypsymphony package build from sou ...
written 8 days ago by
Wolfgang Huber ♦ 13k
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... Lance, this "smells" like a version mismatch problem with the particular instance of R and Bioconductor packages (DEXSeq and its various dependencies) you are using. It's hard to say more or diagnose such things remotely. Can you do one (or both) of the following?
create a minimal working example ...
written 21 days ago by
Wolfgang Huber ♦ 13k
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Comment:
C: IHW multiple testing correction
...
---
title: "Lara Urban IHW question 2018-11-18"
author: "Wolfgang Huber"
output:
BiocStyle::html_document:
toc_float: TRUE
---
# Setup
```{r global_options, include = FALSE}
knitr::opts_chunk$set(cache = TRUE, autodep = TRUE)
options(error = recover)
```
```{r message = FALSE}
library("IHW ...
written 21 days ago by
Wolfgang Huber ♦ 13k
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... Dear Lara
Thanks for the clear posting (reproducible script with small working example, post of the plots).
Indeed it looks like your variable var is not informative on power or prior probability of the tests that generate your p-values. One can glean this from the plot of -log10(p) over rank(var) ...
written 21 days ago by
Wolfgang Huber ♦ 13k
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Comment:
C: IHW multiple testing correction
... The second link should be https://imgur.com/a/prGaWnL - no right parenthesis.
...
written 21 days ago by
Wolfgang Huber ♦ 13k
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... RFC:
I have a question regarding best practice for packages like PGPC, which provides not a general-purpose resource, but a reproducible transcript of the (complete) set of analyses presented in a specific, singular paper (in the case of PGPC, published 2015). That means that it's important for the ...
written 4 weeks ago by
Wolfgang Huber ♦ 13k
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... Save the date!
We would like to announce and invite you to the workshop on Statistical Challenges in Medical Data Science, to be held on 16 – 21 June 2019 at Monte Verità, Ascona, Switzerland. The purpose of the workshop is to bring together participants from statistics, computational sciences, bio ...
written 6 weeks ago by
Wolfgang Huber ♦ 13k
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... How about
overlap <- (red > 0) & (green > 0)
This finds overlapping pixels. If you want to look at cells, you'll need to segment the red image into cells, and subset those cells that overlap in a similar manner.
...
written 11 weeks ago by
Wolfgang Huber ♦ 13k
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... On a more philosophical note, the question "which genes are differentially expressed?" that methods like DESeq2 are trying to answer, is scientifically most meaningful if the answer is relatively sparse, and identifying such genes bears some degree of information content. If almost everything is dif ...
written 12 weeks ago by
Wolfgang Huber ♦ 13k
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134
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... Besides the reasons that Mike mentioned (save memory or compute time) another motivation for filtering can be to improve your multiple testing computations; if that is the motivation, then in fact, you might better off not filtering, but weighting, as e.g. in https://bioconductor.org/packages/releas ...
written 5 months ago by
Wolfgang Huber ♦ 13k
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6 months ago,
created a post with more than 5 votes.
For exprs function - clash with dplyr
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For A: Using DESeq2 normalisation method on a tximport list of matrices without sample
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For Postdocs in Computational Biology / Statistical Data Analysis at EMBL and Univ. Hospital Heidelberg: mechanisms of drug response from ex-vivo large-scale drug testing and multi-omics in cancer
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For Course announcement: CSAMA 2015 (13th ed.) Statistics and Computing in Genome Data Science
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For A: DESeq2 interacting with agricolae
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