User: Joseph Nathaniel Paulson

Reputation:
270
Status:
Trusted
Location:
United States
Twitter:
dorageh
Scholar ID:
Google Scholar Page
Last seen:
1 year, 5 months ago
Joined:
4 years, 6 months ago
Email:
j*******@jimmy.harvard.edu

Posts by Joseph Nathaniel Paulson

<prev • 63 results • page 1 of 7 • next >
0
votes
2
answers
146
views
2
answers
Answer: A: Filter low counts OTUs from a MRfull table to prepare a heatmap
... There's an option in MRfulltable / MRtable called ncounts. Please see the help file for more info. On 2018-01-31 01:46, arguello.rguez [bioc] wrote: > Activity on a post you are following on support.bioconductor.org [1] > > User arguello.rguez [2] wrote Question: Filter low count ...
written 7 months ago by Joseph Nathaniel Paulson270
0
votes
1
answers
177
views
1
answers
Answer: A: Including taxa names in heatmap in metagenomeseq
... Easiest way would probably be to extract the normalized matrix and then put that into plotMRheatmap heatmapColColors = c("grey","green")[as.integer(factor(pd_Donor$Donor))] heatmapCols = colorRampPalette(c("white","light blue","blue","dark blue"))(50) significant_OTU <- which(MRfulltable(Do ...
written 7 months ago by Joseph Nathaniel Paulson270
0
votes
1
answers
257
views
1
answers
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 10 months ago by Joseph Nathaniel Paulson270
0
votes
2
answers
439
views
2
answers
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 17 months ago by Joseph Nathaniel Paulson270
0
votes
3
answers
833
views
3
answers
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 17 months ago by Joseph Nathaniel Paulson270
0
votes
3
answers
833
views
3
answers
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 17 months ago by Joseph Nathaniel Paulson270
0
votes
1
answers
284
views
1
answers
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 17 months ago by Joseph Nathaniel Paulson270
0
votes
3
answers
833
views
3
answers
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 17 months ago by Joseph Nathaniel Paulson270
0
votes
1
answers
239
views
1
answers
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 18 months ago by Joseph Nathaniel Paulson270
0
votes
1
answers
401
views
1
answers
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 20 months ago by Joseph Nathaniel Paulson270

Latest awards to Joseph Nathaniel Paulson

Scholar 2.4 years ago, created an answer that has been accepted. For A: creating a subsetted MRexperiment based on sample name?
Scholar 2.4 years ago, created an answer that has been accepted. For A: Interpretation for MRfulltable of fitzig in Metagenomeseq
Scholar 2.6 years ago, created an answer that has been accepted. For A: creating a subsetted MRexperiment based on sample name?
Scholar 3.1 years ago, created an answer that has been accepted. For A: creating a subsetted MRexperiment based on sample name?

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 236 users visited in the last hour