Showing : metagenomeSeq • reset
0
votes
0
replies
158
views
Help with MetagenomeSeq, understanding the 75th quantile
metagenomeSeq cumulativesumscaling
updated 6 months ago by 68k • written 6 months ago by • 0
0
votes
0
replies
780
views
Try to understand better how to set out an effective sample size within the MetagenomSeq package in microbiome ?
Metagenomics metagenomeSeq microbiome phyloseq microbiomeDataSets
2.0 years ago Mohamed ▴ 30
0
votes
1
reply
1.3k
views
Tool for metagenomic functional analysis with 4-factor study design
Metagenomics DESeq2 metagenomeSeq edgeR KEGG
updated 3.4 years ago by 43k • written 3.4 years ago by • 0
0
votes
0
replies
1.0k
views
Using MetagenomeSeq with intercept gives high logFC
limma metagenomeSeq
4.1 years ago edissepo • 0
0
votes
0
replies
1.4k
views
Pattern Search in MicrobiomeAnalyst
metagenomeSeq Metagenomics microbiome microbiomeExplorer
4.2 years ago GlycineMax • 0
0
votes
0
replies
1.1k
views
Problem with creating an MRexperiment with metagenomeseq - invalid class “MRexperiment” object: 1: feature numbers differ between assayData and featu…
MRexperiment metagenomes metagenomeSeq
4.6 years ago Laura • 0
0
votes
0
replies
1.0k
views
Fitzig function in MetagenomeSeq package
metagenomeSeq fitzig
4.7 years ago Andrew • 0
0
votes
1
reply
1.6k
views
MetagenomeSeq: analysing paired samples
metagenomeseq paired samples microbiome
updated 5.4 years ago by • 0 • written 8.7 years ago by • 0
0
votes
0
replies
1.3k
views
Including covariates with fitFeatureModel
metagenomeSeq
5.8 years ago dkorandla • 0
0
votes
10
replies
2.6k
views
Phyloseq to metagenomeSeq
limma metagenomeSeq
6.3 years ago Jitendra ▴ 10
0
votes
1
reply
1.5k
views
metagenomeSeq error question: error on creation of newMRexperiment
metagenomeseq error metagenomeseq microbiome
6.7 years ago slizo001 • 0
0
votes
1
reply
1.9k
views
[metagenomeSeq] "Error: Warning sample with one or zero features" from cumNormStatFast
metagenomeseq cumNormStatFast features error
7.3 years ago jol.espinoz ▴ 40
0
votes
0
replies
1.3k
views
Paired Difference Analysis
metagenomeseq
7.6 years ago nhua • 0
0
votes
2
replies
1.6k
views
Filter low counts OTUs from a MRfull table to prepare a heatmap
metagenomeseq
7.6 years ago arguello.rguez • 0
1
vote
1
reply
1.5k
views
Including taxa names in heatmap in metagenomeseq
gut microbiome heatmap metagenomeseq
updated 7.6 years ago by ▴ 280 • written 7.6 years ago by • 0
0
votes
1
reply
1.3k
views
metagenomeSeq pre-analysis Data Preporation for full genome sequencing
metagenomeSeq full genome sequencing
updated 7.6 years ago by ▴ 60 • written 7.6 years ago by • 0
1
vote
1
reply
2.2k
views
Should I normalize communities separately with metagenomeseq?
metagenomeseq microbiome gut microbiome metagenomics shotgun metagenomics
updated 7.8 years ago by ▴ 280 • written 7.8 years ago by ▴ 10
0
votes
2
replies
1.7k
views
How do you show/export color scale of a heatmap generated by plotMRheatmap of metagenomeSeq?
metagenomeseq plotmrheatmap color key
8.2 years ago chawonhe • 0
2
votes
6
replies
5.1k
views
Difference between fitFeatureModel and fitZIG in metagenomeSeq
metagenomeseq
8.5 years ago • updated 8.4 years ago sasha • 0
0
votes
1
reply
1.4k
views
metagenomeSeq: role for fitLogNormal?
metagenomeseq
updated 8.4 years ago by ▴ 280 • written 8.4 years ago by ▴ 20
0
votes
2
replies
1.5k
views
metagenomeSeq 1.16.0: unique features give NA's for logFC / p-val?
metagenomeseq
updated 21 months ago by • 0 • written 8.4 years ago by ▴ 20
0
votes
1
reply
1.5k
views
Is it possible to create a Metagenomeseq heatmap with two coloured bars on the top?
metagenomeseq heatmap
updated 8.5 years ago by 68k • written 8.5 years ago by • 0
0
votes
6
replies
2.4k
views
metagenomeSeq log transformation
metagenomeseq logtransformation
updated 8.6 years ago by ▴ 280 • written 8.6 years ago by • 0
0
votes
2
replies
1.8k
views
MetagenomeSeq: Sorting by sample type in plotMRheatmap
metagenomeSeq plotMRheatmap
updated 8.7 years ago by ▴ 280 • written 8.7 years ago by • 0
0
votes
2
replies
1.9k
views
metagenomeSeq: cumNormStat normalization default
metagenomeseq microbiome
8.8 years ago Brian Smith ▴ 120
1
vote
4
replies
1.8k
views
error using fitTimeSeries in metagenomeSeq
metagenomeseq fittimeseries
updated 8.9 years ago by ▴ 280 • written 8.9 years ago by • 0
0
votes
1
reply
1.4k
views
Understand fold changes
metagenomeseq
updated 8.9 years ago by ▴ 280 • written 8.9 years ago by ▴ 860
0
votes
6
replies
3.1k
views
paired analysis using metagenomeSeq
metagenomeseq logfc paired samples standard error
updated 3.1 years ago by • 0 • written 9.0 years ago by ▴ 30
0
votes
5
replies
4.2k
views
DESeq2 16s microbiome size factors
deseq2 metagenomeseq rnaseq 16s microbiome
updated 9.0 years ago by ▴ 280 • written 9.0 years ago by • 0
2
votes
1
reply
2.0k
views
Metagenome seq errors using biom (1.3) file
metagenomeseq qiime biom
updated 9.1 years ago by ▴ 280 • written 9.1 years ago by • 0
0
votes
1
reply
1.2k
views
fitTimeSeries possible error
metagenomeseq fittimeseries
updated 9.1 years ago by ▴ 280 • written 9.1 years ago by • 0
1
vote
2
replies
1.8k
views
metagenomeSeq for continuous phenotype
metagenomeseq continuous limma
9.2 years ago pjgalli2 • 0
0
votes
1
reply
2.0k
views
fitZig coefficient for interaction terms?
metagenomeseq
updated 9.3 years ago by ▴ 280 • written 9.3 years ago by • 0
0
votes
1
reply
1.4k
views
Aggregate By Taxonomy Error
metagenomeSeq
updated 9.3 years ago by ▴ 280 • written 9.3 years ago by • 0
0
votes
5
replies
2.3k
views
MetagenomSeq, perform anova or kruskall wallis with three groups ?
metagenomeseq anova metagenomics
9.3 years ago David ▴ 860
0
votes
3
replies
2.1k
views
Normalisation problem in metagenomeSeq
normalization metagenomeseq
updated 9.4 years ago by ▴ 280 • written 9.4 years ago by ▴ 20
1
vote
1
reply
1.5k
views
Multiple variables in fitFeaturemodel
metagenomeseq
updated 9.5 years ago by ▴ 280 • written 9.5 years ago by • 0
0
votes
0
replies
1.7k
views
Dramatically different results from comparing multiple groups using fitZig versus fitFeatureModel
metagenomeseq
9.5 years ago craemuletz • 0
0
votes
0
replies
1.2k
views
Differential abundance for elevational gradient survey -- use fitTimeSeries?
metagenomeseq
9.5 years ago craemuletz • 0
3
votes
5
replies
3.2k
views
Interpretation for MRfulltable of fitzig in Metagenomeseq
metagenomeseq fitzig MRfulltable
updated 9.6 years ago by ▴ 280 • written 9.6 years ago by • 0
0
votes
6
replies
3.9k
views
Alpha diversity on Rlogtransformed data
deseq2 phyloseq metagenomeseq
9.7 years ago David ▴ 860
1
vote
1
reply
1.4k
views
metagenomeSeq - normFactors
metagenomeseq
updated 9.8 years ago by ▴ 280 • written 9.8 years ago by ▴ 120
1
vote
4
replies
2.2k
views
creating a subsetted MRexperiment based on sample name?
metagenomeseq
updated 10.1 years ago by ▴ 280 • written 10.1 years ago by • 0
4
votes
6
replies
1.9k
views
MetagenomeSeq sparsefeature question
metagenomeseq sparsefeature cumnorm
updated 10.2 years ago by 68k • written 10.2 years ago by • 0
0
votes
7
replies
2.5k
views
metagenomeSeq cumNorm issue with NAs in real data
metagenomeseq
updated 10.4 years ago by ▴ 280 • written 10.4 years ago by • 0
1
vote
1
reply
1.5k
views
Metagenomeseq package; time series analysis
metagenomeseq software error
updated 10.5 years ago by ▴ 280 • written 10.5 years ago by • 0
1
vote
1
reply
1.7k
views
Omission of final edge in correlationTest
metagenomeseq error correlationTest metagenomeseq
10.5 years ago eertel • 0
2
votes
4
replies
2.8k
views
normFactors when aggregating in metagenomeSeq
metagenomeSeq microbiome
updated 2.7 years ago by • 0 • written 10.6 years ago by ▴ 30
1
vote
1
reply
3.6k
views
Low quantile estimate using CSS normalization in metagenomeSeq
metagenomeSeq microbiome
updated 10.6 years ago by ▴ 280 • written 10.6 years ago by ▴ 30
1
vote
1
reply
1.9k
views
Problem reproducing metagenomeSeq tutorial example
metagenome microbiome metagenomeseq
updated 10.6 years ago by ▴ 280 • written 10.6 years ago by ▴ 30
56 results • Page 1 of 2
Recent ...
Replies
Comment: WGCNA analysis on RNAseq and proteoimcs data by sum31278 • 0
Hi sagigordon, Can you share how you performed WGCNA analysis for proteomics data? Thanks
Comment: European Bioconductor Conference 2023 planning by inadequate.peacock.iiag • 0
I once faced a dilemma similar to this when coordinating a smaller local event; despite initial hesitation, I learned invaluable skills and…
Comment: ROAST compare results with complex design by Gordon Smyth 52k
It's also worth pointing out that the syntax for `camera` and `mroast` is the same, so I wonder how OP did the earlier `camera` analysis.
Answer: ROAST compare results with complex design by James W. MacDonald 68k
You are specifying that the last column of your design should be used as the contrast. You should instead use `contrast[,1]`, which will us…
Comment: How to account for solvent controls in DESeq2 when comparing follicular vs lutea by James W. MacDonald 68k
Yes. You can infer that by figuring out what each coefficient measures. Here is your design matrix: ``` > targets ID Name phase G…
Votes
Answer: ROAST compare results with complex design
How to account for solvent controls in DESeq2 when comparing follicular vs luteal phase?
Answer: How to account for solvent controls in DESeq2 when comparing follicular vs lutea
Answer: How to account for solvent controls in DESeq2 when comparing follicular vs lutea
Comment: Using DESeq2 on single cell RNA Seq data of same cell type but different conditi
Awards • All
Popular Question to sum31278 • 0
Popular Question to Gordon Smyth 52k
Popular Question to boczniak767 ▴ 740
Popular Question to Young Tae • 0
Popular Question to Robert Castelo ★ 3.4k
Locations • All
Pittsburgh, United States, 21 minutes ago
United States, 1 hour ago
The city by the bay, 1 hour ago
United States, 1 hour ago
United States, 2 hours ago
Traffic: 851 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6