Showing : metagenomeseq • reset
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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
3 months ago Laura • 0
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0
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70
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Fitzig function in MetagenomeSeq package
metagenomeSeq fitzig
4 months ago Andrew • 0
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1
reply
577
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MetagenomeSeq: analysing paired samples
metagenomeseq paired samples microbiome
updated 13 months ago by • 0 • written 4.4 years ago by • 0
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0
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128
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Including covariates with fitFeatureModel
metagenomeSeq
18 months ago dkorandla • 0
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10
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483
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Phyloseq to metagenomeSeq
limma metagenomeSeq
24 months ago nabiyogesh • 0
0
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1
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363
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metagenomeSeq error question: error on creation of newMRexperiment
metagenomeseq error metagenomeseq microbiome
2.4 years ago slizo001 • 0
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1
reply
543
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[metagenomeSeq] "Error: Warning sample with one or zero features" from cumNormStatFast
metagenomeseq cumNormStatFast features error
3.0 years ago jol.espinoz ▴ 40
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0
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410
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Paired Difference Analysis
metagenomeseq
3.3 years ago nhua • 0
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2
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384
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Filter low counts OTUs from a MRfull table to prepare a heatmap
metagenomeseq
3.3 years ago arguello.rguez • 0
1
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1
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446
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Including taxa names in heatmap in metagenomeseq
gut microbiome heatmap metagenomeseq
updated 3.3 years ago by ▴ 280 • written 3.3 years ago by • 0
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1
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405
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metagenomeSeq pre-analysis Data Preporation for full genome sequencing
metagenomeSeq full genome sequencing
updated 3.3 years ago by ▴ 60 • written 3.3 years ago by • 0
1
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1
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638
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Should I normalize communities separately with metagenomeseq?
metagenomeseq microbiome gut microbiome metagenomics shotgun metagenomics
updated 3.5 years ago by ▴ 280 • written 3.5 years ago by ▴ 10
0
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2
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559
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How do you show/export color scale of a heatmap generated by plotMRheatmap of metagenomeSeq?
metagenomeseq plotmrheatmap color key
3.9 years ago chawonhe • 0
2
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6
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2.2k
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Difference between fitFeatureModel and fitZIG in metagenomeSeq
metagenomeseq
4.1 years ago sasha • 0
0
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1
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543
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metagenomeSeq: role for fitLogNormal?
metagenomeseq
updated 4.1 years ago by ▴ 280 • written 4.1 years ago by ▴ 10
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1
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472
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metagenomeSeq 1.16.0: unique features give NA's for logFC / p-val?
metagenomeseq
updated 4.1 years ago by ▴ 280 • written 4.1 years ago by ▴ 10
0
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1
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557
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Is it possible to create a Metagenomeseq heatmap with two coloured bars on the top?
metagenomeseq heatmap
updated 4.2 years ago by 56k • written 4.2 years ago by • 0
0
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6
replies
814
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metagenomeSeq log transformation
metagenomeseq logtransformation
updated 4.3 years ago by ▴ 280 • written 4.3 years ago by • 0
0
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2
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683
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MetagenomeSeq: Sorting by sample type in plotMRheatmap
metagenomeSeq plotMRheatmap
updated 4.3 years ago by ▴ 280 • written 4.3 years ago by • 0
0
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2
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782
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metagenomeSeq: cumNormStat normalization default
metagenomeseq microbiome
4.5 years ago Brian Smith ▴ 120
1
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4
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604
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error using fitTimeSeries in metagenomeSeq
metagenomeseq fittimeseries
updated 4.6 years ago by ▴ 280 • written 4.6 years ago by • 0
0
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1
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511
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Understand fold changes
metagenomeseq
updated 4.6 years ago by ▴ 280 • written 4.6 years ago by ▴ 860
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5
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1.2k
views
paired analysis using metagenomeSeq
metagenomeseq logfc paired samples standard error
updated 4.6 years ago by • 0 • written 4.6 years ago by ▴ 30
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5
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2.0k
views
DESeq2 16s microbiome size factors
deseq2 metagenomeseq rnaseq 16s microbiome
updated 4.7 years ago by ▴ 280 • written 4.7 years ago by • 0
2
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1
reply
801
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Metagenome seq errors using biom (1.3) file
metagenomeseq qiime biom
updated 4.8 years ago by ▴ 280 • written 4.8 years ago by • 0
0
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1
reply
447
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fitTimeSeries possible error
metagenomeseq fittimeseries
updated 4.8 years ago by ▴ 280 • written 4.8 years ago by • 0
1
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2
replies
636
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metagenomeSeq for continuous phenotype
metagenomeseq continuous limma
4.8 years ago pjgalli2 • 0
0
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1
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1.2k
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fitZig coefficient for interaction terms?
metagenomeseq
updated 5.0 years ago by ▴ 280 • written 5.0 years ago by • 0
0
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1
reply
467
views
Aggregate By Taxonomy Error
metagenomeSeq
updated 5.0 years ago by ▴ 280 • written 5.0 years ago by • 0
0
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5
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870
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MetagenomSeq, perform anova or kruskall wallis with three groups ?
metagenomeseq anova metagenomics
5.0 years ago David ▴ 860
0
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3
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905
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Normalisation problem in metagenomeSeq
normalization metagenomeseq
updated 5.1 years ago by ▴ 280 • written 5.1 years ago by ▴ 20
1
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1
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652
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Multiple variables in fitFeaturemodel
metagenomeseq
updated 5.2 years ago by ▴ 280 • written 5.2 years ago by • 0
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0
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788
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Dramatically different results from comparing multiple groups using fitZig versus fitFeatureModel
metagenomeseq
5.2 years ago craemuletz • 0
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0
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533
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Differential abundance for elevational gradient survey -- use fitTimeSeries?
metagenomeseq
5.2 years ago craemuletz • 0
3
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5
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1.4k
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Interpretation for MRfulltable of fitzig in Metagenomeseq
metagenomeseq fitzig MRfulltable
updated 5.3 years ago by ▴ 280 • written 5.3 years ago by • 0
0
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6
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1.6k
views
Alpha diversity on Rlogtransformed data
deseq2 phyloseq metagenomeseq
5.4 years ago David ▴ 860
1
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1
reply
634
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metagenomeSeq - normFactors
metagenomeseq
updated 5.5 years ago by ▴ 280 • written 5.5 years ago by ▴ 120
1
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4
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920
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creating a subsetted MRexperiment based on sample name?
metagenomeseq
updated 5.8 years ago by ▴ 280 • written 5.8 years ago by • 0
4
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6
replies
687
views
MetagenomeSeq sparsefeature question
metagenomeseq sparsefeature cumnorm
updated 5.9 years ago by 56k • written 5.9 years ago by • 0
0
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7
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980
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metagenomeSeq cumNorm issue with NAs in real data
metagenomeseq
updated 6.1 years ago by ▴ 280 • written 6.1 years ago by • 0
1
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1
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617
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Metagenomeseq package; time series analysis
metagenomeseq software error
updated 6.1 years ago by ▴ 280 • written 6.1 years ago by • 0
1
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1
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784
views
Omission of final edge in correlationTest
metagenomeseq error correlationTest metagenomeseq
6.2 years ago eertel • 0
2
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3
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1.3k
views
normFactors when aggregating in metagenomeSeq
metagenomeSeq microbiome
updated 6.3 years ago by ▴ 280 • written 6.3 years ago by ▴ 30
1
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1
reply
2.0k
views
Low quantile estimate using CSS normalization in metagenomeSeq
metagenomeSeq microbiome
updated 6.3 years ago by ▴ 280 • written 6.3 years ago by ▴ 30
1
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1
reply
916
views
Problem reproducing metagenomeSeq tutorial example
metagenome microbiome metagenomeseq
updated 6.3 years ago by ▴ 280 • written 6.3 years ago by ▴ 10
2
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2
replies
671
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no timeInterval output using fitTimeSeries
metagenomeSeq fitTimeSeries microbiome
6.3 years ago noelle.noyes ▴ 30
2
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2
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866
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error using fitTimeSeries from metagenomeSeq
metagenomeSeq microbiome
6.3 years ago noelle.noyes ▴ 30
2
votes
1
reply
1.4k
views
metagenomeSeq error using cumNormStatFast
metagenomeSeq
updated 6.3 years ago by ▴ 280 • written 6.3 years ago by ▴ 30
0
votes
1
reply
887
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mouseData in heatmap of metagenomeSeq package
Metagenomics metagenomeSeq Metagenomics metagenomeSeq
updated 7.2 years ago by ▴ 280 • written 7.2 years ago by ★ 12k
0
votes
1
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778
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error on heatmap
PROMISE metagenomeSeq PROMISE metagenomeSeq
updated 7.2 years ago by ▴ 280 • written 7.2 years ago by ★ 12k
50 results • Page 1 of 1
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Comment: Warning in EnhancedVolcano plot by Kevin Blighe 2.9k
Thanks - that is interesting to know.
Comment: Warning in EnhancedVolcano plot by charles.feigin ▴ 20
Sorry, one more quick reply. So, changing lengthConnectors and/or directionConnectors doesn't let me render any more connectors, but I foun…
Comment: Warning in EnhancedVolcano plot by charles.feigin ▴ 20
Ok I understand. I'll play around with these. Thank you!
Answer: How to make OrgPackage (BSgenome data) package available for R Bioconductor user by Hervé Pagès 14k
What organisms are they?
Comment: "dim<-" against on-disk arrays by Hervé Pagès 14k
I will look into this although I don't promise anything. Even though many of the operations supported by standard arrays can be implemented…
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Comment: Warning in EnhancedVolcano plot
Comment: Warning in EnhancedVolcano plot
Comment: Warning in EnhancedVolcano plot
Comment: Warning in EnhancedVolcano plot
A: How to make a (limma) heatmap displaying gene ID's as rownames
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