User: gabriel.hoffman

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30
Status:
New User
Location:
United States
Website:
http://gabrielhoffman....
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Google Scholar Page
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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Comment: C: BiocParallel: What its the best way to pass large a dataset for parallel process
... I really appreciate your detailed answer Cheers, - Gabriel ...
written 27 days ago by gabriel.hoffman30
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Comment: C: BiocParallel: What its the best way to pass large a dataset for parallel process
... 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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BiocParallel: What its the best way to pass large a dataset for parallel processing?
... 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 ...
biocparallel bioconductor bplapply bpiterate iterator written 29 days ago by gabriel.hoffman30 • updated 28 days ago by Martin Morgan ♦♦ 23k
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Answer: A: Blocking factor in limma/voom vs. variancePartition/dream analysis.
... 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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Bug report for GenomicRanges
... 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 ...
genomicranges written 9 months ago by gabriel.hoffman30 • updated 9 months ago by Michael Lawrence11k
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Gene set enrichment analysis with ChIP-seq data using test statistics directly
... 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 ...
limma csaw written 11 months ago by gabriel.hoffman30 • updated 11 months ago by Aaron Lun24k
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Answer: A: Making package compatible with old version of R/Bioconductor
... 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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Making package compatible with old version of R/Bioconductor
... 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 ...
biocinstaller software error R bioconductor 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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