Showing : metagenomeseq • reset
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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
16 months ago Mohamed ▴ 30
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1
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1.1k
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Tool for metagenomic functional analysis with 4-factor study design
Metagenomics DESeq2 metagenomeSeq edgeR KEGG
updated 2.7 years ago by 43k • written 2.7 years ago by • 0
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853
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Using MetagenomeSeq with intercept gives high logFC
limma metagenomeSeq
3.4 years ago edissepo • 0
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1.2k
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Pattern Search in MicrobiomeAnalyst
metagenomeSeq Metagenomics microbiome microbiomeExplorer
3.5 years ago GlycineMax • 0
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956
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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
3.9 years ago Laura • 0
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885
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Fitzig function in MetagenomeSeq package
metagenomeSeq fitzig
4.0 years ago Andrew • 0
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1
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1.4k
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MetagenomeSeq: analysing paired samples
metagenomeseq paired samples microbiome
updated 4.7 years ago by • 0 • written 8.1 years ago by • 0
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1.2k
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Including covariates with fitFeatureModel
metagenomeSeq
5.2 years ago dkorandla • 0
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10
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2.3k
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Phyloseq to metagenomeSeq
limma metagenomeSeq
5.6 years ago Jitendra ▴ 10
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1
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1.3k
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metagenomeSeq error question: error on creation of newMRexperiment
metagenomeseq error metagenomeseq microbiome
6.0 years ago slizo001 • 0
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1
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1.7k
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[metagenomeSeq] "Error: Warning sample with one or zero features" from cumNormStatFast
metagenomeseq cumNormStatFast features error
6.6 years ago jol.espinoz ▴ 40
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1.2k
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Paired Difference Analysis
metagenomeseq
6.9 years ago nhua • 0
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2
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1.4k
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Filter low counts OTUs from a MRfull table to prepare a heatmap
metagenomeseq
6.9 years ago arguello.rguez • 0
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1
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1.4k
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Including taxa names in heatmap in metagenomeseq
gut microbiome heatmap metagenomeseq
updated 6.9 years ago by ▴ 280 • written 6.9 years ago by • 0
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1
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1.2k
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metagenomeSeq pre-analysis Data Preporation for full genome sequencing
metagenomeSeq full genome sequencing
updated 7.0 years ago by ▴ 60 • written 7.0 years ago by • 0
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1
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2.0k
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Should I normalize communities separately with metagenomeseq?
metagenomeseq microbiome gut microbiome metagenomics shotgun metagenomics
updated 7.1 years ago by ▴ 280 • written 7.1 years ago by ▴ 10
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2
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1.5k
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How do you show/export color scale of a heatmap generated by plotMRheatmap of metagenomeSeq?
metagenomeseq plotmrheatmap color key
7.5 years ago chawonhe • 0
2
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6
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4.7k
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Difference between fitFeatureModel and fitZIG in metagenomeSeq
metagenomeseq
7.8 years ago sasha • 0
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1
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1.3k
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metagenomeSeq: role for fitLogNormal?
metagenomeseq
updated 7.8 years ago by ▴ 280 • written 7.8 years ago by ▴ 20
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2
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1.3k
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metagenomeSeq 1.16.0: unique features give NA's for logFC / p-val?
metagenomeseq
updated 13 months ago by • 0 • written 7.8 years ago by ▴ 20
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1
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1.4k
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Is it possible to create a Metagenomeseq heatmap with two coloured bars on the top?
metagenomeseq heatmap
updated 7.8 years ago by 67k • written 7.8 years ago by • 0
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6
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2.2k
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metagenomeSeq log transformation
metagenomeseq logtransformation
updated 7.9 years ago by ▴ 280 • written 7.9 years ago by • 0
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2
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1.7k
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MetagenomeSeq: Sorting by sample type in plotMRheatmap
metagenomeSeq plotMRheatmap
updated 8.0 years ago by ▴ 280 • written 8.0 years ago by • 0
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2
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1.7k
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metagenomeSeq: cumNormStat normalization default
metagenomeseq microbiome
8.1 years ago Brian Smith ▴ 120
1
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4
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1.6k
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error using fitTimeSeries in metagenomeSeq
metagenomeseq fittimeseries
updated 8.2 years ago by ▴ 280 • written 8.2 years ago by • 0
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1
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1.3k
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Understand fold changes
metagenomeseq
updated 8.2 years ago by ▴ 280 • written 8.2 years ago by ▴ 860
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6
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2.8k
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paired analysis using metagenomeSeq
metagenomeseq logfc paired samples standard error
updated 2.4 years ago by • 0 • written 8.3 years ago by ▴ 30
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5
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3.9k
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DESeq2 16s microbiome size factors
deseq2 metagenomeseq rnaseq 16s microbiome
updated 8.3 years ago by ▴ 280 • written 8.3 years ago by • 0
2
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1
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1.8k
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Metagenome seq errors using biom (1.3) file
metagenomeseq qiime biom
updated 8.4 years ago by ▴ 280 • written 8.4 years ago by • 0
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1
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1.1k
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fitTimeSeries possible error
metagenomeseq fittimeseries
updated 8.4 years ago by ▴ 280 • written 8.4 years ago by • 0
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2
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1.6k
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metagenomeSeq for continuous phenotype
metagenomeseq continuous limma
8.5 years ago pjgalli2 • 0
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1
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1.8k
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fitZig coefficient for interaction terms?
metagenomeseq
updated 8.6 years ago by ▴ 280 • written 8.6 years ago by • 0
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1
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1.2k
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Aggregate By Taxonomy Error
metagenomeSeq
updated 8.6 years ago by ▴ 280 • written 8.6 years ago by • 0
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5
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2.1k
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MetagenomSeq, perform anova or kruskall wallis with three groups ?
metagenomeseq anova metagenomics
8.6 years ago David ▴ 860
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3
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1.9k
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Normalisation problem in metagenomeSeq
normalization metagenomeseq
updated 8.7 years ago by ▴ 280 • written 8.7 years ago by ▴ 20
1
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1
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1.4k
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Multiple variables in fitFeaturemodel
metagenomeseq
updated 8.8 years ago by ▴ 280 • written 8.8 years ago by • 0
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1.6k
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Dramatically different results from comparing multiple groups using fitZig versus fitFeatureModel
metagenomeseq
8.9 years ago craemuletz • 0
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0
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1.1k
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Differential abundance for elevational gradient survey -- use fitTimeSeries?
metagenomeseq
8.9 years ago craemuletz • 0
3
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5
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2.9k
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Interpretation for MRfulltable of fitzig in Metagenomeseq
metagenomeseq fitzig MRfulltable
updated 8.9 years ago by ▴ 280 • written 8.9 years ago by • 0
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6
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3.6k
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Alpha diversity on Rlogtransformed data
deseq2 phyloseq metagenomeseq
9.1 years ago David ▴ 860
1
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1
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1.3k
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metagenomeSeq - normFactors
metagenomeseq
updated 9.1 years ago by ▴ 280 • written 9.1 years ago by ▴ 120
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4
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2.0k
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creating a subsetted MRexperiment based on sample name?
metagenomeseq
updated 9.4 years ago by ▴ 280 • written 9.4 years ago by • 0
4
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6
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1.7k
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MetagenomeSeq sparsefeature question
metagenomeseq sparsefeature cumnorm
updated 9.5 years ago by 67k • written 9.5 years ago by • 0
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7
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2.3k
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metagenomeSeq cumNorm issue with NAs in real data
metagenomeseq
updated 9.7 years ago by ▴ 280 • written 9.7 years ago by • 0
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1
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1.3k
views
Metagenomeseq package; time series analysis
metagenomeseq software error
updated 9.8 years ago by ▴ 280 • written 9.8 years ago by • 0
1
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1
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1.6k
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Omission of final edge in correlationTest
metagenomeseq error correlationTest metagenomeseq
9.9 years ago eertel • 0
2
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4
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2.6k
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normFactors when aggregating in metagenomeSeq
metagenomeSeq microbiome
updated 2.0 years ago by • 0 • written 9.9 years ago by ▴ 30
1
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1
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3.3k
views
Low quantile estimate using CSS normalization in metagenomeSeq
metagenomeSeq microbiome
updated 9.9 years ago by ▴ 280 • written 9.9 years ago by ▴ 30
1
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1
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1.8k
views
Problem reproducing metagenomeSeq tutorial example
metagenome microbiome metagenomeseq
updated 9.9 years ago by ▴ 280 • written 9.9 years ago by ▴ 30
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2
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1.5k
views
no timeInterval output using fitTimeSeries
metagenomeSeq fitTimeSeries microbiome
10.0 years ago noelle.noyes ▴ 30
50 results • Page 1 of 1
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Comment: minfi latest update for EPIC V2 chip by macdonaldfrench7286566 • 0
Yes, the most updated analysis for the EPIC V2 chip using the minfi package still involves using the annotations provided by jokergoo. *Th…
Answer: Incorporating Salmon offset matrix into Wilcoxon DEG analysis by Gordon Smyth 52k
To compute CPM values from edgeR: ``` y <- DGEList(counts = counts, samples = samples, genes = genes, group = samples$Disease_status) y <- …
Comment: edgeR + tximport: calcNormFactors and the usage of offsets by Gordon Smyth 52k
Follow the vignette. It explains how to call edgeR's cpm function to use the offsets.
Comment: edgeR + tximport: calcNormFactors and the usage of offsets by Andre • 0
But if i want to do another type of analysis like Wilcoxon/Mann-Whitney and want to incorporate salmon offset can i simply use the cpm func…
Comment: DESeq error: counts matrix should be numeric, currently it has mode: character by Kucsera • 0
After applying your suggestion, the following error pops up: ``` Error in mde(x) : 'list' object cannot be coerced to type 'double' ```
Votes
A: GWAS analysis with Illumina HumanOmni5-4 BeadChip - recommended software and wor
A: GWAS analysis with Illumina HumanOmni5-4 BeadChip - recommended software and wor
A: RNA-seq Normalisation - normalise all samples in experiment or only the ones use
Answer: Can DESeq2's design compensate for sequencing experimental design shortcomings?
Comment: Issues with seqlevelsStyle when making custom txdb objects for genomes/annotatio
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