User: gabriel.hoffman

Reputation:
30
Status:
New User
Location:
United States
Website:
http://gabrielhoffman....
Scholar ID:
Last seen:
1 week, 1 day ago
Joined:
4 years, 1 month ago
Email:
g**************@mssm.edu

I develop and apply statistical methods in genomics (mostly RNA-Seq) to understand the biology of human disease.

Posts by gabriel.hoffman

<prev • 8 results • page 1 of 1 • next >
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written 27 days ago by gabriel.hoffman30
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... Hi Martin, Thanks for your quick response! Yes, this was just example code, so lmFit() would solve this specific problem, but not my real problem. Your last paragraph gets at my underlying question: How do I get bplapply() to run in parallel when I pass it an iterator? Can I define my itera ...
written 28 days ago by gabriel.hoffman30
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... I have a large gene expression matrix and would like to perform some analysis on each row (i.e. gene) at a time using parallel processing from BiocParallel. Since the matrix can be very large, I figured that using bplapply() with SnowParam(workers=12, "SOCK") and a custom iterator would enabl ...
written 29 days ago by gabriel.hoffman30 • updated 28 days ago by Martin Morgan ♦♦ 23k
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... Hi Ben, Thanks for your comment. Both limma and dream analysis include two steps: 1) estimate weights, 2) fit regression model using these weights. The limma/voom workflow uses voom() and then lmFit(). The dream package focuses on replacing lmFit() with dream() in order to model random e ...
written 7 weeks ago by gabriel.hoffman30
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... GenomicRanges prints a large set of warnings to my terminal when I set a class variable first: library(GenomicRanges) setClass("DataFrame") gr = GRanges(rep(1, 2), IRanges(1:2, 1:2)) This results in this message printed to the terminal: Found more than one class "DataFrame" in cache; using th ...
written 9 months ago by gabriel.hoffman30 • updated 9 months ago by Michael Lawrence11k
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... In RNA-seq/microarray data, enrichment analysis of gene sets generally takes 2 forms:  1) Identify a set of genes that are significant by some metric (usually FDR < 5%) and evaluate enrichment compared to some background set of genes; 2) use the test statistics directly to avoid an arbitrary cuto ...
written 11 months ago by gabriel.hoffman30 • updated 11 months ago by Aaron Lun24k
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... I really appreciate your feedback.  I agree with you, I just wanted to see if I was missing anything Thanks, - Gabriel  ...
written 3.2 years ago by gabriel.hoffman30
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... I wrote the Bioconductor package variancePartition (http://bioconductor.org/packages/variancePartition/) which is currently available for Bioconductor >=v3.2 and corresponds to R >=v3.2.  I submitted a manuscript based on this software to a peer-reviewed journal, but a reviewer only has R v3.1 ...
written 3.2 years ago by gabriel.hoffman30

Latest awards to gabriel.hoffman

Scholar 8 months ago, created an answer that has been accepted. For A: Blocking factor in limma/voom vs. variancePartition/dream analysis.
Autobiographer 3.1 years ago, has more than 80 characters in the information field of the user's profile.

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