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User: Michael Steinbaugh

Reputation:
20
Status:
New User
Location:
Harvard
Website:
https://steinbaugh.com/
Twitter:
mjsteinbaugh
Scholar ID:
Google Scholar Page
Last seen:
15 hours ago
Joined:
2 years, 7 months ago
Email:
m***@steinbaugh.com

Posts by Michael Steinbaugh

<prev • 11 results • page 1 of 2 • next >
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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 10 days 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 10 days ago by Michael Steinbaugh20 • updated 10 days ago by Marcel Ramos ♦♦ 350
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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 21 days ago by Michael Steinbaugh20 • updated 21 days ago by Michael Love22k
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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 11 weeks 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 11 weeks 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 11 weeks 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 3 months ago by Michael Steinbaugh20 • updated 3 months ago by shepherl ♦♦ 1.1k
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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 6 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 21 months ago by Michael Steinbaugh20
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Answer: A: BiomaRt package not working
... The Ensembl website is down for maintenance, which could also be causing your biomaRt requests to error out at the moment. ...
written 22 months ago by Michael Steinbaugh20

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