User: Hector Corrada Bravo

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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 12 weeks 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 3 months ago by Hector Corrada Bravo60
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Comment: C: Phyloseq to metagenomeSeq
... That's right, that should work. ...
written 3 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 3 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 3 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 3 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 18 months ago by Hector Corrada Bravo60
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Answer: A: metagenomeSeq pre-analysis Data Preporation for full genome sequencing
... 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 20 months ago by Hector Corrada Bravo60
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What's new in epiviz
... 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 ...
epivizr metavizr written 2.3 years ago by Hector Corrada Bravo60
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Answer: A: Survey on interactive visualization and Bioconductor
... 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 3.2 years ago by Hector Corrada Bravo60

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