Showing : metagenomeSeq • reset
4
votes
6
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1.5k
views
MetagenomeSeq sparsefeature question
metagenomeseq sparsefeature cumnorm
updated 8.8 years ago by 65k • written 8.8 years ago by • 0
3
votes
5
replies
2.5k
views
Interpretation for MRfulltable of fitzig in Metagenomeseq
metagenomeseq fitzig MRfulltable
updated 8.2 years ago by ▴ 280 • written 8.2 years ago by • 0
2
votes
2
replies
1.3k
views
no timeInterval output using fitTimeSeries
metagenomeSeq fitTimeSeries microbiome
9.3 years ago noelle.noyes ▴ 30
2
votes
6
replies
4.1k
views
Difference between fitFeatureModel and fitZIG in metagenomeSeq
metagenomeseq
7.1 years ago • updated 7.0 years ago sasha • 0
2
votes
4
replies
2.3k
views
normFactors when aggregating in metagenomeSeq
metagenomeSeq microbiome
updated 16 months ago by • 0 • written 9.2 years ago by ▴ 30
2
votes
1
reply
1.6k
views
Metagenome seq errors using biom (1.3) file
metagenomeseq qiime biom
updated 7.7 years ago by ▴ 280 • written 7.7 years ago by • 0
2
votes
1
reply
2.5k
views
metagenomeSeq error using cumNormStatFast
metagenomeSeq
updated 9.3 years ago by ▴ 280 • written 9.3 years ago by ▴ 30
2
votes
2
replies
1.5k
views
error using fitTimeSeries from metagenomeSeq
metagenomeSeq microbiome
9.3 years ago noelle.noyes ▴ 30
1
vote
1
reply
1.4k
views
Omission of final edge in correlationTest
metagenomeseq error correlationTest metagenomeseq
9.2 years ago eertel • 0
1
vote
2
replies
1.4k
views
metagenomeSeq for continuous phenotype
metagenomeseq continuous limma
7.8 years ago pjgalli2 • 0
1
vote
1
reply
1.1k
views
Metagenomeseq package; time series analysis
metagenomeseq software error
updated 9.1 years ago by ▴ 280 • written 9.1 years ago by • 0
1
vote
1
reply
1.2k
views
metagenomeSeq - normFactors
metagenomeseq
updated 8.4 years ago by ▴ 280 • written 8.4 years ago by ▴ 120
1
vote
1
reply
1.2k
views
Multiple variables in fitFeaturemodel
metagenomeseq
updated 8.1 years ago by ▴ 280 • written 8.1 years ago by • 0
1
vote
1
reply
1.6k
views
Problem reproducing metagenomeSeq tutorial example
metagenome microbiome metagenomeseq
updated 9.2 years ago by ▴ 280 • written 9.2 years ago by ▴ 30
1
vote
4
replies
1.3k
views
error using fitTimeSeries in metagenomeSeq
metagenomeseq fittimeseries
updated 7.5 years ago by ▴ 280 • written 7.5 years ago by • 0
1
vote
1
reply
3.0k
views
Low quantile estimate using CSS normalization in metagenomeSeq
metagenomeSeq microbiome
updated 9.2 years ago by ▴ 280 • written 9.2 years ago by ▴ 30
1
vote
1
reply
1.7k
views
Should I normalize communities separately with metagenomeseq?
metagenomeseq microbiome gut microbiome metagenomics shotgun metagenomics
updated 6.4 years ago by ▴ 280 • written 6.4 years ago by ▴ 10
1
vote
4
replies
1.7k
views
creating a subsetted MRexperiment based on sample name?
metagenomeseq
updated 8.7 years ago by ▴ 280 • written 8.7 years ago by • 0
1
vote
1
reply
1.1k
views
Including taxa names in heatmap in metagenomeseq
gut microbiome heatmap metagenomeseq
updated 6.2 years ago by ▴ 280 • written 6.2 years ago by • 0
0
votes
6
replies
1.8k
views
metagenomeSeq log transformation
metagenomeseq logtransformation
updated 7.2 years ago by ▴ 280 • written 7.2 years ago by • 0
0
votes
1
reply
1.1k
views
Is it possible to create a Metagenomeseq heatmap with two coloured bars on the top?
metagenomeseq heatmap
updated 7.1 years ago by 65k • written 7.1 years ago by • 0
0
votes
2
replies
1.1k
views
metagenomeSeq 1.16.0: unique features give NA's for logFC / p-val?
metagenomeseq
updated 4 months ago by • 0 • written 7.1 years ago by ▴ 10
0
votes
1
reply
1.1k
views
metagenomeSeq: role for fitLogNormal?
metagenomeseq
updated 7.1 years ago by ▴ 280 • written 7.1 years ago by ▴ 10
0
votes
2
replies
1.3k
views
How do you show/export color scale of a heatmap generated by plotMRheatmap of metagenomeSeq?
metagenomeseq plotmrheatmap color key
6.8 years ago chawonhe • 0
0
votes
1
reply
990
views
metagenomeSeq pre-analysis Data Preporation for full genome sequencing
metagenomeSeq full genome sequencing
updated 6.3 years ago by ▴ 60 • written 6.3 years ago by • 0
0
votes
2
replies
1.1k
views
Filter low counts OTUs from a MRfull table to prepare a heatmap
metagenomeseq
6.2 years ago arguello.rguez • 0
0
votes
0
replies
963
views
Paired Difference Analysis
metagenomeseq
6.2 years ago nhua • 0
0
votes
1
reply
1.4k
views
[metagenomeSeq] "Error: Warning sample with one or zero features" from cumNormStatFast
metagenomeseq cumNormStatFast features error
5.9 years ago jol.espinoz ▴ 40
0
votes
1
reply
1.1k
views
metagenomeSeq error question: error on creation of newMRexperiment
metagenomeseq error metagenomeseq microbiome
5.3 years ago slizo001 • 0
0
votes
0
replies
882
views
Including covariates with fitFeatureModel
metagenomeSeq
4.5 years ago dkorandla • 0
0
votes
0
replies
689
views
Fitzig function in MetagenomeSeq package
metagenomeSeq fitzig
3.3 years ago Andrew • 0
0
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0
replies
771
views
Problem with creating an MRexperiment with metagenomeseq - invalid class “MRexperiment” object: 1: feature numbers differ between assayData and featu…
MRexperiment metagenomes metagenomeSeq
3.2 years ago Laura • 0
0
votes
1
reply
801
views
Tool for metagenomic functional analysis with 4-factor study design
Metagenomics DESeq2 metagenomeSeq edgeR KEGG
updated 2.0 years ago by 41k • written 2.0 years ago by • 0
0
votes
0
replies
626
views
Using MetagenomeSeq with intercept gives high logFC
limma metagenomeSeq
2.7 years ago edissepo • 0
0
votes
0
replies
940
views
Pattern Search in MicrobiomeAnalyst
metagenomeSeq Metagenomics microbiome microbiomeExplorer
2.8 years ago GlycineMax • 0
0
votes
0
replies
1.4k
views
Dramatically different results from comparing multiple groups using fitZig versus fitFeatureModel
metagenomeseq
8.2 years ago craemuletz • 0
0
votes
0
replies
351
views
Try to understand better how to set out an effective sample size within the MetagenomSeq package in microbiome ?
Metagenomics metagenomeSeq microbiome phyloseq microbiomeDataSets
8 months ago Mohamed ▴ 30
0
votes
5
replies
3.5k
views
DESeq2 16s microbiome size factors
deseq2 metagenomeseq rnaseq 16s microbiome
updated 7.6 years ago by ▴ 280 • written 7.6 years ago by • 0
0
votes
10
replies
1.8k
views
Phyloseq to metagenomeSeq
limma metagenomeSeq
4.9 years ago Jitendra ▴ 10
0
votes
0
replies
1.1k
views
metagenomeSeq paper out in Nature Methods
Normalization metagenomeSeq Normalization metagenomeSeq
10.6 years ago Hector Corrada Bravo ▴ 40
0
votes
1
reply
1.4k
views
error on heatmap
PROMISE metagenomeSeq PROMISE metagenomeSeq
updated 10.1 years ago by ▴ 280 • written 10.1 years ago by ★ 13k
0
votes
1
reply
1.5k
views
mouseData in heatmap of metagenomeSeq package
Metagenomics metagenomeSeq Metagenomics metagenomeSeq
updated 10.1 years ago by ▴ 280 • written 10.1 years ago by ★ 13k
0
votes
7
replies
1.9k
views
metagenomeSeq cumNorm issue with NAs in real data
metagenomeseq
updated 9.0 years ago by ▴ 280 • written 9.0 years ago by • 0
0
votes
6
replies
3.2k
views
Alpha diversity on Rlogtransformed data
deseq2 phyloseq metagenomeseq
8.4 years ago David ▴ 860
0
votes
0
replies
975
views
Differential abundance for elevational gradient survey -- use fitTimeSeries?
metagenomeseq
8.2 years ago craemuletz • 0
0
votes
3
replies
1.6k
views
Normalisation problem in metagenomeSeq
normalization metagenomeseq
updated 8.0 years ago by ▴ 280 • written 8.0 years ago by ▴ 20
0
votes
5
replies
1.8k
views
MetagenomSeq, perform anova or kruskall wallis with three groups ?
metagenomeseq anova metagenomics
7.9 years ago David ▴ 860
0
votes
1
reply
1.0k
views
Aggregate By Taxonomy Error
metagenomeSeq
updated 7.9 years ago by ▴ 280 • written 7.9 years ago by • 0
0
votes
1
reply
1.7k
views
fitZig coefficient for interaction terms?
metagenomeseq
updated 7.9 years ago by ▴ 280 • written 7.9 years ago by • 0
0
votes
1
reply
911
views
fitTimeSeries possible error
metagenomeseq fittimeseries
updated 7.7 years ago by ▴ 280 • written 7.7 years ago by • 0
50 results • Page 1 of 1
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Comment: Finding DEGs by using edgeR by Gordon Smyth 50k
Filtering (removing lowly expressed genes) is separate to normalization. It isn't clear why not subsetting would cause any difficulty. It …
Comment: How to make DGEList and design matrix by edgeR package by prity6459 • 0
Thank you for your suggestion. Yes, I have made DGEList and design matrix in my script. But I was not entirely confident while making thos…
Comment: Finding DEGs by using edgeR by prity6459 • 0
Hello Gordon, Thanks for your response. By normalization, I meant that I have already removed lowly expressed genes from my count matrix. …
Answer: FilterByExpr low counts with small sample size by Gordon Smyth 50k
It doesn't seem to me that there is necessarily any problem with the analysis. You say that there are "too many low-reads" but actually th…
Answer: How to make DGEList and design matrix by edgeR package by Gordon Smyth 50k
Your question is curious because you showed code that made a DGEList and design matrix in your previous post just 15 hours ago. Please h…
Votes
Answer: OrgDb for maize
Comment: significant difference of p-values with dream() after updating VariancePartition
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
Comment: DEXSeq DEXSeqDataSet count matrix duplication
Comment: Error in champ.load(): The following specified files do not exist
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