User: Michael Steinbaugh

Reputation:
20
Status:
New User
Location:
Harvard
Website:
https://steinbaugh.com/
Twitter:
mjsteinbaugh
Scholar ID:
Google Scholar Page
Last seen:
1 week, 5 days ago
Joined:
2 years, 9 months ago
Email:
m***@steinbaugh.com

Posts by Michael Steinbaugh

<prev • 12 results • page 1 of 2 • next >
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Comment: C: DESeq2 lfcShrink using only dds and res arguments
... Jason, try passing in a `coef` or `contrast` argument along with the `res` in your `lfcShrink()` call. ...
written 13 days ago by Michael Steinbaugh20
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Comment: C: Proper way to deprecate an S4 generic
... Thanks Marcel. I've started consolidating my S4 generics into a single pacakge when applicable, similar to the BiocGenerics approach. I'm trying to be extremely conservative deprecating generics, but there are a few edge cases where the verbs aren't quite as clear as another spelling, and I want to ...
written 9 weeks ago by Michael Steinbaugh20
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Proper way to deprecate an S4 generic
... What's the current best practice for deprecating an S4 generic? Is something along the lines of this approach recommended? ``` setGeneric( name = "A", def = function(object, ...) { .Deprecated("B") standardGeneric("B") } ) setGeneric( name = "B", def = function( ...
s4 generic written 9 weeks ago by Michael Steinbaugh20 • updated 9 weeks ago by Marcel Ramos ♦♦ 360
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DESeq2 lfcShrink using only dds and res arguments
... Hi Mike, According to the DESeq2 `lfcShrink()` documentation, it appears that the function should work when you provide a `DESeqDataSet` (`dds`) and corresponding `DESeqResults` (`res`) generated using the standard `DESeq() %>% results()` approach, correct? On BioC 3.8 (v1.22.2), I'm seeing this ...
deseq2 written 11 weeks ago by Michael Steinbaugh20 • updated 11 weeks ago by Michael Love23k
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Comment: C: How to clear a cached S4 method
... Indeed, I think that's what I'm seeing in my library. I'm working on reinstalling the dependencies from scratch to see if that fixes the issue. Thanks Martin! ...
written 4 months ago by Michael Steinbaugh20
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Comment: C: How to clear a cached S4 method
... As a follow-up, I've found some additional information in How Methods Work regarding how S4 generics cache methods, but there's very little information in the R documentation on how to troubleshoot S4 caching issues. I'm working on trying to generate a reprex for this issue, but it does seem to be ...
written 4 months ago by Michael Steinbaugh20
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How to clear a cached S4 method
... I seem to have hit an S4 method caching issue on R 3.5.1 / Bioconductor 3.8 that appears to be specific to Linux. I can reproduce this issue on the Bioc 3.8 release AMI as well as a VM running Red Hat Linux. Running the same version of R/Bioconductor on macOS with the same versions of my toolchain d ...
s4 devtools methods cache written 4 months ago by Michael Steinbaugh20
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GenomicFeatures won't install for 3.8 release
... I seem to be running into a bug with GenomicFeatures installation for Bioconductor 3.8 (Red Hat Linux 3.10.0-957.el7.x86_64): > BiocManager::install("GenomicFeatures", version = "3.8") Bioconductor version 3.8 (BiocManager 1.30.3), R 3.5.1 (2018-07-02) Installing package(s) 'GenomicFeatures' ...
installation biocmanager written 5 months ago by Michael Steinbaugh20 • updated 5 months ago by shepherl ♦♦ 1.3k
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Comment: C: ZINB-WaVE + DESeq2 misses low-expressed, single-condition genes that look like t
... I think Wolfgang Huber mentioned that about UMI counts right? I'm running a DE analysis using zimbwave and will look out for this too. Thanks Rory. ...
written 8 months ago by Michael Steinbaugh20
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Answer: A: BiocCheck path escape issue
... Thanks I'll be sure to post anything like this to bioc-devel in the future. ...
written 23 months ago by Michael Steinbaugh20

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