User: Joseph Nathaniel Paulson

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Posts by Joseph Nathaniel Paulson

<prev • 61 results • page 1 of 7 • next >
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Answer: A: Should I normalize communities separately with metagenomeseq?
... I would do them together, though I guess it won't make much of a difference as the quantile chosen will likely fall to default and then you're calculating a sample specific scalar. On 2017-11-17 03:49, lilianeconteville [bioc] wrote: > Activity on a post you are following on support.biocond ...
written 4 days ago by Joseph Nathaniel Paulson260
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Answer: A: Where to find open access microbiome data for case-control comparative study?
... Here are two that are available: https://bioconductor.org/packages/release/data/experiment/html/msd16s.html https://bioconductor.org/packages/release/data/experiment/html/etec16s.html Within metagenomeSeq (https://bioconductor.org/packages/release/bioc/html/metagenomeSeq.html) there are also two s ...
written 7 months ago by Joseph Nathaniel Paulson260
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Comment: C: Difference between fitFeatureModel and fitZIG in metagenomeSeq
... Yes, thank you for the suggestion. Will add a note that this feature is not available yet. For the next release I will definitely modify the vignette. It's become a bit of a hodgepodge of added tests over the last year or so. A bit of restructuring will be good. As before, thanks will work on it ...
written 7 months ago by Joseph Nathaniel Paulson260
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Comment: C: Difference between fitFeatureModel and fitZIG in metagenomeSeq
... The fitZig output is analogous to Limma's topTable output due to historical reasons and how closely fitZig was built on top of the lmFit function. The column title is intended to be the coefficient of interest (as logFC is really just the estimate the coefficient of interest in our case). I agree th ...
written 7 months ago by Joseph Nathaniel Paulson260
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Answer: A: metagenomeSeq: role for fitLogNormal?
... MetagenomeSeq has a number of tests implemented and available for users, including Fisher's exact test for presence / absence of a feature (fitPA) and a measure of the discovery odds (based on # reads) (fitDO). fitFeatureModel does not call fitLogNormal. fitLogNormal is solely a permutation based t ...
written 7 months ago by Joseph Nathaniel Paulson260
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Answer: A: Difference between fitFeatureModel and fitZIG in metagenomeSeq
... There is a bit of a confusion that I will try to address. fitZig and fitFeatureModel provide two different methods. fitZig is the approach described in http://www.nature.com/nmeth/journal/v10/n12/full/nmeth.2658.html. fitFeatureModel is described in Chapter 4 of Normalization and differential abund ...
written 7 months ago by Joseph Nathaniel Paulson260
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Answer: A: metagenomeSeq 1.16.0: unique features give NA's for logFC / p-val?
... The fitFeatureModel will return NA p-values for any features where there are less than 3 positive samples in a group. The full model is not estimable otherwise.   Will modify this later once I have a bit more time. ...
written 7 months ago by Joseph Nathaniel Paulson260
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Comment: C: metagenomeSeq log transformation
... This normalization step is not expected input for metagenomeSeq and it was not designed for that. The method was designed for read counts that you can read up on in the supplementary material here: http://www.nature.com/nmeth/journal/v10/n12/full/nmeth.2658.html. Or in the vignette. ...
written 10 months ago by Joseph Nathaniel Paulson260
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Comment: C: metagenomeSeq log transformation
... That means you're not putting counts in. Log of a fraction will lead to a negative number. On Jan 21, 2017 5:26 PM, "PJ [bioc]" <noreply@bioconductor.org> wrote:Activity on a post you are following on support.bioconductor.org User PJ wrote C: metagenomeSeq log transformation: Thanks ...
written 10 months ago by Joseph Nathaniel Paulson260
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Answer: A: metagenomeSeq log transformation
... To extract raw, or normalized counts, the MRcounts function is used. If you just type MRcounts you'll see that we use a continuity-correction pseudocount of 1. This maps 0s --> 0s in log-space. ...
written 10 months ago by Joseph Nathaniel Paulson260

Latest awards to Joseph Nathaniel Paulson

Scholar 19 months ago, created an answer that has been accepted. For A: creating a subsetted MRexperiment based on sample name?
Scholar 19 months ago, created an answer that has been accepted. For A: Interpretation for MRfulltable of fitzig in Metagenomeseq
Scholar 21 months ago, created an answer that has been accepted. For A: creating a subsetted MRexperiment based on sample name?
Scholar 2.3 years ago, created an answer that has been accepted. For A: creating a subsetted MRexperiment based on sample name?

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