User: Joseph Bundy

gravatar for Joseph Bundy
Joseph Bundy20
Reputation:
20
Status:
New User
Location:
United States
Last seen:
4 months ago
Joined:
3 years, 11 months ago
Email:
j***********@gmail.com

Posts by Joseph Bundy

<prev • 8 results • page 1 of 1 • next >
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Answer: A: DESeq2 rlog function takes too long
... Hi there, I've been encountering similar problems with long wait times on certain R functions (especially those in DEXSeq and WGCNA), and I have only 60 samples. If waiting around on R is a problem you're facing often, I might give Intel MKL libraries a look, discussed here: http://brettklamer.com/ ...
written 3.8 years ago by Joseph Bundy20
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Comment: C: DEXSeq: DEXSeqHTML, plotDEXSeq and interaction tests
... Thanks Alejandro! ...
written 3.9 years ago by Joseph Bundy20
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DEXSeq: DEXSeqHTML, plotDEXSeq and interaction tests
... Hello all, Following the advice in this post: https://support.bioconductor.org/p/74871/#74927 , I have been using DEXSeq to analyze mouse samples of different biological sex and age. I specified the sex:time interaction in the design formula and the testForDEU() function seems to have progressed wi ...
dexseq written 3.9 years ago by Joseph Bundy20 • updated 3.9 years ago by Alejandro Reyes1.7k
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Comment: C: RUVseq PCA on raw data, whereas DESeq suggests stabilization
... What the package can do for you I think really depends on what functions you make use of.  Re: sequencing depth, between lane normalization is covered on page 3 of the RUVseq vignette:  https://www.bioconductor.org/packages/3.3/bioc/vignettes/RUVSeq/inst/doc/RUVSeq.pdf set <- betweenLaneNormaliz ...
written 3.9 years ago by Joseph Bundy20
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Comment: C: DEXSeq and Independent filtering
... Thanks for the advice Dr. Huber,    Adhering closely to the DESeq2 vignette (which has been very, very helpful) and the bioconductor RNA-seq workflow page, I've performed most of the exploratory analyses I can think of.  There is considerable variation in sequencing depth across my full experiment ...
written 3.9 years ago by Joseph Bundy20
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Comment: C: DEXSeq and Independent filtering
... Thanks for your help Alejandro!  You understood my objective perfectly. Thanks for taking the time to read my very long post. I will likely take you up on your suggestion to test the interaction.  -Joseph ...
written 3.9 years ago by Joseph Bundy20
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DEXSeq and Independent filtering
... Hello, I’m getting some curious results from DEXSeq and am trying to get some perspective / advice. I am conducting an analysis of age-differences in female and male mice.  I have samples from mice of two ages and both sexes (two factors, two levels, n = 5). For the purposes of this post, I am inte ...
genefilter dexseq deseq2 written 3.9 years ago by Joseph Bundy20 • updated 3.9 years ago by Wolfgang Huber13k
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Answer: A: DEXSeqHTML filenames gone wrong
... This is my first post, so I apologize if it's a little unorthodox or inappropriately formatted.  I am running into the same error as Jannetta, and I believe that I have identified the problem.  When exporting the report with DEXSeqHTML(), the .html and .svg files have "files" appended to the name ...
written 3.9 years ago by Joseph Bundy20

Latest awards to Joseph Bundy

Popular Question 2.0 years ago, created a question with more than 1,000 views. For DEXSeq and Independent filtering
Supporter 3.9 years ago, voted at least 25 times.

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