Showing : metagenomeseq • reset
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Help with MetagenomeSeq, understanding the 75th quantile
metagenomeSeq cumulativesumscaling
updated 3 months ago by 68k • written 3 months ago by • 0
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710
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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
21 months ago Mohamed ▴ 30
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1.2k
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Tool for metagenomic functional analysis with 4-factor study design
Metagenomics DESeq2 metagenomeSeq edgeR KEGG
updated 3.1 years ago by 43k • written 3.1 years ago by • 0
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961
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Using MetagenomeSeq with intercept gives high logFC
limma metagenomeSeq
3.8 years ago edissepo • 0
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1.3k
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Pattern Search in MicrobiomeAnalyst
metagenomeSeq Metagenomics microbiome microbiomeExplorer
3.9 years ago GlycineMax • 0
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1.0k
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Problem with creating an MRexperiment with metagenomeseq - invalid class “MRexperiment” object: 1: feature numbers differ between assayData and featu…
MRexperiment metagenomes metagenomeSeq
4.3 years ago Laura • 0
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996
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Fitzig function in MetagenomeSeq package
metagenomeSeq fitzig
4.4 years ago Andrew • 0
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1
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1.5k
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MetagenomeSeq: analysing paired samples
metagenomeseq paired samples microbiome
updated 5.1 years ago by • 0 • written 8.5 years ago by • 0
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1.2k
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Including covariates with fitFeatureModel
metagenomeSeq
5.5 years ago dkorandla • 0
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10
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2.5k
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Phyloseq to metagenomeSeq
limma metagenomeSeq
6.0 years ago Jitendra ▴ 10
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1
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1.4k
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metagenomeSeq error question: error on creation of newMRexperiment
metagenomeseq error metagenomeseq microbiome
6.4 years ago slizo001 • 0
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1
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1.8k
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[metagenomeSeq] "Error: Warning sample with one or zero features" from cumNormStatFast
metagenomeseq cumNormStatFast features error
7.0 years ago jol.espinoz ▴ 40
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1.3k
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Paired Difference Analysis
metagenomeseq
7.3 years ago nhua • 0
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2
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1.5k
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Filter low counts OTUs from a MRfull table to prepare a heatmap
metagenomeseq
7.3 years ago arguello.rguez • 0
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1.5k
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Including taxa names in heatmap in metagenomeseq
gut microbiome heatmap metagenomeseq
updated 7.3 years ago by ▴ 280 • written 7.3 years ago by • 0
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1
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1.3k
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metagenomeSeq pre-analysis Data Preporation for full genome sequencing
metagenomeSeq full genome sequencing
updated 7.3 years ago by ▴ 60 • written 7.3 years ago by • 0
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2.2k
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Should I normalize communities separately with metagenomeseq?
metagenomeseq microbiome gut microbiome metagenomics shotgun metagenomics
updated 7.5 years ago by ▴ 280 • written 7.5 years ago by ▴ 10
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2
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1.6k
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How do you show/export color scale of a heatmap generated by plotMRheatmap of metagenomeSeq?
metagenomeseq plotmrheatmap color key
7.9 years ago chawonhe • 0
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6
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5.0k
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Difference between fitFeatureModel and fitZIG in metagenomeSeq
metagenomeseq
8.2 years ago • updated 8.1 years ago sasha • 0
0
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1
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1.3k
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metagenomeSeq: role for fitLogNormal?
metagenomeseq
updated 8.1 years ago by ▴ 280 • written 8.1 years ago by ▴ 20
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2
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1.4k
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metagenomeSeq 1.16.0: unique features give NA's for logFC / p-val?
metagenomeseq
updated 17 months ago by • 0 • written 8.2 years ago by ▴ 20
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1
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1.5k
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Is it possible to create a Metagenomeseq heatmap with two coloured bars on the top?
metagenomeseq heatmap
updated 8.2 years ago by 68k • written 8.2 years ago by • 0
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6
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2.3k
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metagenomeSeq log transformation
metagenomeseq logtransformation
updated 8.3 years ago by ▴ 280 • written 8.3 years ago by • 0
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2
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1.8k
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MetagenomeSeq: Sorting by sample type in plotMRheatmap
metagenomeSeq plotMRheatmap
updated 8.4 years ago by ▴ 280 • written 8.4 years ago by • 0
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2
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1.8k
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metagenomeSeq: cumNormStat normalization default
metagenomeseq microbiome
8.5 years ago Brian Smith ▴ 120
1
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4
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1.7k
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error using fitTimeSeries in metagenomeSeq
metagenomeseq fittimeseries
updated 8.6 years ago by ▴ 280 • written 8.6 years ago by • 0
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1
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1.4k
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Understand fold changes
metagenomeseq
updated 8.6 years ago by ▴ 280 • written 8.6 years ago by ▴ 860
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6
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3.0k
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paired analysis using metagenomeSeq
metagenomeseq logfc paired samples standard error
updated 2.8 years ago by • 0 • written 8.7 years ago by ▴ 30
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5
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4.0k
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DESeq2 16s microbiome size factors
deseq2 metagenomeseq rnaseq 16s microbiome
updated 8.7 years ago by ▴ 280 • written 8.7 years ago by • 0
2
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1
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1.9k
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Metagenome seq errors using biom (1.3) file
metagenomeseq qiime biom
updated 8.8 years ago by ▴ 280 • written 8.8 years ago by • 0
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1
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1.2k
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fitTimeSeries possible error
metagenomeseq fittimeseries
updated 8.8 years ago by ▴ 280 • written 8.8 years ago by • 0
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2
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1.7k
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metagenomeSeq for continuous phenotype
metagenomeseq continuous limma
8.9 years ago pjgalli2 • 0
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1
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1.9k
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fitZig coefficient for interaction terms?
metagenomeseq
updated 9.0 years ago by ▴ 280 • written 9.0 years ago by • 0
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1
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1.3k
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Aggregate By Taxonomy Error
metagenomeSeq
updated 9.0 years ago by ▴ 280 • written 9.0 years ago by • 0
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5
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2.3k
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MetagenomSeq, perform anova or kruskall wallis with three groups ?
metagenomeseq anova metagenomics
9.0 years ago David ▴ 860
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3
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2.0k
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Normalisation problem in metagenomeSeq
normalization metagenomeseq
updated 9.1 years ago by ▴ 280 • written 9.1 years ago by ▴ 20
1
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1
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1.5k
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Multiple variables in fitFeaturemodel
metagenomeseq
updated 9.2 years ago by ▴ 280 • written 9.2 years ago by • 0
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1.7k
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Dramatically different results from comparing multiple groups using fitZig versus fitFeatureModel
metagenomeseq
9.2 years ago craemuletz • 0
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1.2k
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Differential abundance for elevational gradient survey -- use fitTimeSeries?
metagenomeseq
9.2 years ago craemuletz • 0
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5
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3.0k
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Interpretation for MRfulltable of fitzig in Metagenomeseq
metagenomeseq fitzig MRfulltable
updated 9.3 years ago by ▴ 280 • written 9.3 years ago by • 0
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6
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3.8k
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Alpha diversity on Rlogtransformed data
deseq2 phyloseq metagenomeseq
9.4 years ago David ▴ 860
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1
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1.4k
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metagenomeSeq - normFactors
metagenomeseq
updated 9.5 years ago by ▴ 280 • written 9.5 years ago by ▴ 120
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4
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2.1k
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creating a subsetted MRexperiment based on sample name?
metagenomeseq
updated 9.8 years ago by ▴ 280 • written 9.8 years ago by • 0
4
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6
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1.8k
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MetagenomeSeq sparsefeature question
metagenomeseq sparsefeature cumnorm
updated 9.9 years ago by 68k • written 9.9 years ago by • 0
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7
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2.4k
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metagenomeSeq cumNorm issue with NAs in real data
metagenomeseq
updated 10.1 years ago by ▴ 280 • written 10.1 years ago by • 0
1
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1
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1.4k
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Metagenomeseq package; time series analysis
metagenomeseq software error
updated 10.2 years ago by ▴ 280 • written 10.2 years ago by • 0
1
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1
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1.7k
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Omission of final edge in correlationTest
metagenomeseq error correlationTest metagenomeseq
10.3 years ago eertel • 0
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4
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2.8k
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normFactors when aggregating in metagenomeSeq
metagenomeSeq microbiome
updated 2.4 years ago by • 0 • written 10.3 years ago by ▴ 30
1
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1
reply
3.5k
views
Low quantile estimate using CSS normalization in metagenomeSeq
metagenomeSeq microbiome
updated 10.3 years ago by ▴ 280 • written 10.3 years ago by ▴ 30
1
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1
reply
1.8k
views
Problem reproducing metagenomeSeq tutorial example
metagenome microbiome metagenomeseq
updated 10.3 years ago by ▴ 280 • written 10.3 years ago by ▴ 30
50 results • Page 1 of 1
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Answer: Typo in the help of lmFit() by Gordon Smyth 52k
Thanks for the heads-up. > The _Details_ in the documentation of lmFit() still says that the default correlation is 0.75 Yes, you're righ…
Comment: Adding gene names as row annotations to an RNAseq heatmap made with ComplexHeatm by caroline.zanchi ▴ 10
Thank you ! ![enter image description here][1] In the end I did ```r rn2 <- select(org.Dm.eg.db, row.names(cent_expr_matrix), "GENENAME"…
Answer: Memory issue while using "quickcluster" and "computeSumFactors" functions on sin by James W. MacDonald 68k
The obvious solution is to use cloud computing, which is likely cheaper than getting more RAM for your computer.
Answer: Adding gene names as row annotations to an RNAseq heatmap made with ComplexHeatm by James W. MacDonald 68k
``` library(org.Dm.eg.db) rn <- select(org.Dm.eg.db, row.names(cent_expr_matrix), "SYMBOL","FLYBASE") ## ensure no NA values get propaga…
Comment: Discrepancies in normalised count data vs unnormalised by AMgroup • 0
Thank you for your explanation, that makes sense. Do you have any suggestions on how to deal with this issue? if it is an issue? especially…
Votes
Answer: Adding gene names as row annotations to an RNAseq heatmap made with ComplexHeatm
Answer: Adding gene names as row annotations to an RNAseq heatmap made with ComplexHeatm
Deseq2 DE analysis of host-pathogen samples (model separately or jointly?)
Comment: Check removeBatchEffect effectiveness
Answer: Check removeBatchEffect effectiveness
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