## User: Hector Corrada Bravo

Reputation:
60
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Location:
United States
Website:
http://cbcb.umd.edu/~h...
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4 months, 3 weeks ago
Joined:
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#### Posts by Hector Corrada Bravo

<prev • 18 results • page 1 of 2 • next >
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Comment: C: Phyloseq to metagenomeSeq
... They are equivalent more or less. The latter gives you more control over how normalization is done. Also, please consider using wrenchNorm instead of cumNorm which we have seen works well. ...
written 4 months ago by Hector Corrada Bravo60
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Comment: C: Phyloseq to metagenomeSeq
... Use the MRcounts function to get counts, it has arguments to specify normalized and/or logged counts. ...
written 5 months ago by Hector Corrada Bravo60
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Comment: C: Phyloseq to metagenomeSeq
... That's right, that should work. ...
written 5 months ago by Hector Corrada Bravo60
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Comment: C: Phyloseq to metagenomeSeq
... You should leave as default. If there was a convergence issue, you will see a warning, in which case you can set to a larger value. In my experience, things converge very quickly for most datasets. ...
written 5 months ago by Hector Corrada Bravo60
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Comment: C: Phyloseq to metagenomeSeq
... You should leave as default. If there was a convergence issue, you will see a warning, in which case you can set to a larger value. In my experience, things converge very quickly for most datasets. ...
written 5 months ago by Hector Corrada Bravo60
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Comment: C: Phyloseq to metagenomeSeq
... Thank you for writing, please excuse the delay in answering: 1) Not knowing how you got to the phyloseq object, I am unable to answer the normalization question. In general, we recommend that you normalize data using cumNorm or (newly added wrenchNorm) functions. 2) You should not set maxit=1 ...
written 5 months ago by Hector Corrada Bravo60
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Answer: A: cpgCollapse in Minfi
... When argument ‘returnBlockInfo=TRUE’ that information is returned as well. In your example, it is included in collapsingGset[[2]]` On Mar 5, 2018, 12:21 PM -0500, cbartle3 [bioc] <noreply@bioconductor.org>, wrote: > Activity on a post you are following on support.bioconductor.org > Use ...
written 20 months ago by Hector Corrada Bravo60
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... metagenomeSeq assumes you have a count matrix for features of interest (genes or taxa). Look at tools like kraken or metaphlan2 to create a count matrix. Hector On Jan 15, 2018, 8:56 PM -0500, cmapoulton [bioc] <noreply@bioconductor.org>, wrote: > Activity on a post you are following on su ...
written 22 months ago by Hector Corrada Bravo60
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... The most recent Bioconductor version includes updates to epivizr and a new package, metavizr, for interactive visualization of metagenomic data. We wrote a post describing these, and took the opportunity to update on other developments in the Epiviz project.   https://epiviz.github.io/post/2017-05 ...
written 2.5 years ago by Hector Corrada Bravo60
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... We want to share results from this survey during developer day at the upcoming BioC 2016. We've had great participation but want to encourage those who haven't taken the survey yet to consider doing so in the next couple of days. https://umdsurvey.umd.edu/SE/?SID=SV_5bXhBBZ8cKY08yp Thanks! Hector ...
written 3.4 years ago by Hector Corrada Bravo60

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