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metagenomeseq
•
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0
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replies
321
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Try to understand better how to set out an effective sample size within the MetagenomSeq package in microbiome ?
Metagenomics
metagenomeSeq
microbiome
phyloseq
microbiomeDataSets
7 months ago
Mohamed
▴ 30
0
votes
1
reply
754
views
Tool for metagenomic functional analysis with 4-factor study design
Metagenomics
DESeq2
metagenomeSeq
edgeR
KEGG
updated 23 months ago by
Michael Love
41k • written 23 months ago by
Aditya
• 0
0
votes
0
replies
609
views
Using MetagenomeSeq with intercept gives high logFC
limma
metagenomeSeq
2.7 years ago
edissepo
• 0
0
votes
0
replies
908
views
Pattern Search in MicrobiomeAnalyst
metagenomeSeq
Metagenomics
microbiome
microbiomeExplorer
2.7 years ago
GlycineMax
• 0
0
votes
0
replies
751
views
Problem with creating an MRexperiment with metagenomeseq - invalid class “MRexperiment” object: 1: feature numbers differ between assayData and featu…
MRexperiment
metagenomes
metagenomeSeq
3.1 years ago
Laura
• 0
0
votes
0
replies
665
views
Fitzig function in MetagenomeSeq package
metagenomeSeq
fitzig
3.2 years ago
Andrew
• 0
0
votes
1
reply
1.2k
views
MetagenomeSeq: analysing paired samples
metagenomeseq
paired samples
microbiome
updated 4.0 years ago by
jananee15
• 0 • written 7.3 years ago by
marypadilha
• 0
0
votes
0
replies
853
views
Including covariates with fitFeatureModel
metagenomeSeq
4.4 years ago
dkorandla
• 0
0
votes
10
replies
1.8k
views
Phyloseq to metagenomeSeq
limma
metagenomeSeq
4.8 years ago
Jitendra
▴ 10
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
1
reply
1.3k
views
[metagenomeSeq] "Error: Warning sample with one or zero features" from cumNormStatFast
metagenomeseq
cumNormStatFast
features
error
5.8 years ago
jol.espinoz
▴ 40
0
votes
0
replies
942
views
Paired Difference Analysis
metagenomeseq
6.1 years ago
nhua
• 0
0
votes
2
replies
1.1k
views
Filter low counts OTUs from a MRfull table to prepare a heatmap
metagenomeseq
6.1 years ago
arguello.rguez
• 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
Joseph Nathaniel Paulson
▴ 280 • written 6.2 years ago by
arguello.rguez
• 0
0
votes
1
reply
959
views
metagenomeSeq pre-analysis Data Preporation for full genome sequencing
metagenomeSeq
full genome sequencing
updated 6.2 years ago by
Hector Corrada Bravo
▴ 60 • written 6.2 years ago by
cmapoulton
• 0
1
vote
1
reply
1.7k
views
Should I normalize communities separately with metagenomeseq?
metagenomeseq
microbiome
gut microbiome
metagenomics
shotgun metagenomics
updated 6.3 years ago by
Joseph Nathaniel Paulson
▴ 280 • written 6.3 years ago by
lilianeconteville
▴ 10
0
votes
2
replies
1.2k
views
How do you show/export color scale of a heatmap generated by plotMRheatmap of metagenomeSeq?
metagenomeseq
plotmrheatmap
color key
6.7 years ago
chawonhe
• 0
2
votes
6
replies
4.0k
views
Difference between fitFeatureModel and fitZIG in metagenomeSeq
metagenomeseq
7.0 years ago
sasha
• 0
0
votes
1
reply
1.1k
views
metagenomeSeq: role for fitLogNormal?
metagenomeseq
updated 7.0 years ago by
Joseph Nathaniel Paulson
▴ 280 • written 7.0 years ago by
handibles
▴ 10
0
votes
2
replies
1.1k
views
metagenomeSeq 1.16.0: unique features give NA's for logFC / p-val?
metagenomeseq
updated 3 months ago by
liqiong464
• 0 • written 7.0 years ago by
handibles
▴ 10
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 7.0 years ago by
James W. MacDonald
65k • written 7.0 years ago by
Key
• 0
0
votes
6
replies
1.8k
views
metagenomeSeq log transformation
metagenomeseq
logtransformation
updated 7.2 years ago by
Joseph Nathaniel Paulson
▴ 280 • written 7.2 years ago by
PJ
• 0
0
votes
2
replies
1.4k
views
MetagenomeSeq: Sorting by sample type in plotMRheatmap
metagenomeSeq
plotMRheatmap
updated 7.2 years ago by
Joseph Nathaniel Paulson
▴ 280 • written 7.2 years ago by
Rachael
• 0
0
votes
2
replies
1.5k
views
metagenomeSeq: cumNormStat normalization default
metagenomeseq
microbiome
7.3 years ago
Brian Smith
▴ 120
1
vote
4
replies
1.3k
views
error using fitTimeSeries in metagenomeSeq
metagenomeseq
fittimeseries
updated 7.4 years ago by
Joseph Nathaniel Paulson
▴ 280 • written 7.4 years ago by
wijera81
• 0
0
votes
1
reply
1.0k
views
Understand fold changes
metagenomeseq
updated 7.5 years ago by
Joseph Nathaniel Paulson
▴ 280 • written 7.5 years ago by
David
▴ 860
0
votes
6
replies
2.5k
views
paired analysis using metagenomeSeq
metagenomeseq
logfc
paired samples
standard error
updated 20 months ago by
tom830979
• 0 • written 7.5 years ago by
manasishah86
▴ 30
0
votes
5
replies
3.5k
views
DESeq2 16s microbiome size factors
deseq2
metagenomeseq
rnaseq
16s
microbiome
updated 7.6 years ago by
Joseph Nathaniel Paulson
▴ 280 • written 7.6 years ago by
jbatsx
• 0
2
votes
1
reply
1.5k
views
Metagenome seq errors using biom (1.3) file
metagenomeseq
qiime
biom
updated 7.6 years ago by
Joseph Nathaniel Paulson
▴ 280 • written 7.6 years ago by
dr.richrodrigues
• 0
0
votes
1
reply
893
views
fitTimeSeries possible error
metagenomeseq
fittimeseries
updated 7.6 years ago by
Joseph Nathaniel Paulson
▴ 280 • written 7.6 years ago by
giulia.masetti
• 0
1
vote
2
replies
1.3k
views
metagenomeSeq for continuous phenotype
metagenomeseq
continuous
limma
7.7 years ago
pjgalli2
• 0
0
votes
1
reply
1.7k
views
fitZig coefficient for interaction terms?
metagenomeseq
updated 7.8 years ago by
Joseph Nathaniel Paulson
▴ 280 • written 7.8 years ago by
nhuda6
• 0
0
votes
1
reply
1.0k
views
Aggregate By Taxonomy Error
metagenomeSeq
updated 7.8 years ago by
Joseph Nathaniel Paulson
▴ 280 • written 7.8 years ago by
nhuda6
• 0
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
3
replies
1.6k
views
Normalisation problem in metagenomeSeq
normalization
metagenomeseq
updated 7.9 years ago by
Joseph Nathaniel Paulson
▴ 280 • written 7.9 years ago by
Stephen Rolfe
▴ 20
1
vote
1
reply
1.2k
views
Multiple variables in fitFeaturemodel
metagenomeseq
updated 8.1 years ago by
Joseph Nathaniel Paulson
▴ 280 • written 8.1 years ago by
sajancr
• 0
0
votes
0
replies
1.4k
views
Dramatically different results from comparing multiple groups using fitZig versus fitFeatureModel
metagenomeseq
8.1 years ago
craemuletz
• 0
0
votes
0
replies
951
views
Differential abundance for elevational gradient survey -- use fitTimeSeries?
metagenomeseq
8.1 years ago
craemuletz
• 0
3
votes
5
replies
2.4k
views
Interpretation for MRfulltable of fitzig in Metagenomeseq
metagenomeseq
fitzig
MRfulltable
updated 8.1 years ago by
Joseph Nathaniel Paulson
▴ 280 • written 8.1 years ago by
Han-Na Kim
• 0
0
votes
6
replies
3.1k
views
Alpha diversity on Rlogtransformed data
deseq2
phyloseq
metagenomeseq
8.3 years ago
David
▴ 860
1
vote
1
reply
1.1k
views
metagenomeSeq - normFactors
metagenomeseq
updated 8.4 years ago by
Joseph Nathaniel Paulson
▴ 280 • written 8.4 years ago by
Brian Smith
▴ 120
1
vote
4
replies
1.6k
views
creating a subsetted MRexperiment based on sample name?
metagenomeseq
updated 8.6 years ago by
Joseph Nathaniel Paulson
▴ 280 • written 8.6 years ago by
rleonzay
• 0
4
votes
6
replies
1.4k
views
MetagenomeSeq sparsefeature question
metagenomeseq
sparsefeature
cumnorm
updated 8.7 years ago by
James W. MacDonald
65k • written 8.7 years ago by
yang.xiang1030
• 0
0
votes
7
replies
1.9k
views
metagenomeSeq cumNorm issue with NAs in real data
metagenomeseq
updated 8.9 years ago by
Joseph Nathaniel Paulson
▴ 280 • written 8.9 years ago by
carr0603
• 0
1
vote
1
reply
1.1k
views
Metagenomeseq package; time series analysis
metagenomeseq
software error
updated 9.0 years ago by
Joseph Nathaniel Paulson
▴ 280 • written 9.0 years ago by
pvp2101
• 0
1
vote
1
reply
1.4k
views
Omission of final edge in correlationTest
metagenomeseq error
correlationTest
metagenomeseq
9.1 years ago
eertel
• 0
2
votes
4
replies
2.2k
views
normFactors when aggregating in metagenomeSeq
metagenomeSeq
microbiome
updated 15 months ago by
Muhammad
• 0 • written 9.1 years ago by
noelle.noyes
▴ 30
1
vote
1
reply
3.0k
views
Low quantile estimate using CSS normalization in metagenomeSeq
metagenomeSeq
microbiome
updated 9.2 years ago by
Joseph Nathaniel Paulson
▴ 280 • written 9.2 years ago by
noelle.noyes
▴ 30
1
vote
1
reply
1.5k
views
Problem reproducing metagenomeSeq tutorial example
metagenome
microbiome
metagenomeseq
updated 9.2 years ago by
Joseph Nathaniel Paulson
▴ 280 • written 9.2 years ago by
jovel_juan
▴ 30
2
votes
2
replies
1.3k
views
no timeInterval output using fitTimeSeries
metagenomeSeq
fitTimeSeries
microbiome
9.2 years ago
noelle.noyes
▴ 30
50 results • Page
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Comment: Unable to annotate ExpressionSet object from hugene11st chip
by
James W. MacDonald
65k
Let's take a closer look. ``` > library(GEOquery) ## some random data > getGEOSuppFiles("GSE193983") > setwd("GSE193983/") > untar("GSE19…
Comment: DEG Filtering
by
Gordon Smyth
50k
RMA normalization is good but batch correction using NOISeq isn't right. Data shouldn't be batch corrected before the limma analysis and NO…
Answer: maftools: Error in validateMaf(maf = maf, isTCGA = isTCGA, rdup = removeDuplicat
by
snijesh
▴ 20
You can try: using `read.delim` or `fread`. ``` my_maf = data.table::fread("path/to/maf/sample.maf") my_maf = read.maf(maf = my_maf) …
Comment: DEG Filtering
by
Amit
• 0
Hi Gordon, Thank you for your response and advice. I want to analyze Dataset GSE18090 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi) whic…
Comment: edgeR, 3 x 2 design with a batch effect and contrasts
by
Gordon Smyth
50k
Yes, that is a quote from [A guide to creating design matrices for gene expression experiments](https://bioconductor.org/packages/release/w…
Votes
Comment: DEG Filtering
Answer: DEG Filtering
Answer: DEG Filtering
Answer: edgeR, 3 x 2 design with a batch effect and contrasts
Answer: padj-based gradient scale from barplot (clusterProfiler results) does not work p
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