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
8 months ago Mohamed ▴ 30
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1
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813
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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
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631
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Using MetagenomeSeq with intercept gives high logFC
limma metagenomeSeq
2.8 years ago edissepo • 0
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0
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950
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Pattern Search in MicrobiomeAnalyst
metagenomeSeq Metagenomics microbiome microbiomeExplorer
2.8 years ago GlycineMax • 0
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0
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773
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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
3.2 years ago Laura • 0
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0
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692
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Fitzig function in MetagenomeSeq package
metagenomeSeq fitzig
3.3 years ago Andrew • 0
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1
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1.2k
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MetagenomeSeq: analysing paired samples
metagenomeseq paired samples microbiome
updated 4.1 years ago by • 0 • written 7.4 years ago by • 0
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0
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889
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Including covariates with fitFeatureModel
metagenomeSeq
4.5 years ago dkorandla • 0
0
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10
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1.9k
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Phyloseq to metagenomeSeq
limma metagenomeSeq
4.9 years ago Jitendra ▴ 10
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1
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1.1k
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metagenomeSeq error question: error on creation of newMRexperiment
metagenomeseq error metagenomeseq microbiome
5.4 years ago slizo001 • 0
0
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1
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1.4k
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[metagenomeSeq] "Error: Warning sample with one or zero features" from cumNormStatFast
metagenomeseq cumNormStatFast features error
5.9 years ago jol.espinoz ▴ 40
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0
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967
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Paired Difference Analysis
metagenomeseq
6.2 years ago nhua • 0
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2
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1.1k
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Filter low counts OTUs from a MRfull table to prepare a heatmap
metagenomeseq
6.2 years ago arguello.rguez • 0
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1
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1.1k
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Including taxa names in heatmap in metagenomeseq
gut microbiome heatmap metagenomeseq
updated 6.3 years ago by ▴ 280 • written 6.3 years ago by • 0
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1
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993
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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
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1
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1.7k
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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
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2
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1.3k
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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
2
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6
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4.1k
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Difference between fitFeatureModel and fitZIG in metagenomeSeq
metagenomeseq
7.1 years ago sasha • 0
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1
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1.1k
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metagenomeSeq: role for fitLogNormal?
metagenomeseq
updated 7.1 years ago by ▴ 280 • written 7.1 years ago by ▴ 10
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2
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1.1k
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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
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1
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1.1k
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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
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6
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1.8k
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metagenomeSeq log transformation
metagenomeseq logtransformation
updated 7.3 years ago by ▴ 280 • written 7.3 years ago by • 0
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2
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1.4k
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MetagenomeSeq: Sorting by sample type in plotMRheatmap
metagenomeSeq plotMRheatmap
updated 7.3 years ago by ▴ 280 • written 7.3 years ago by • 0
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2
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1.5k
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metagenomeSeq: cumNormStat normalization default
metagenomeseq microbiome
7.4 years ago Brian Smith ▴ 120
1
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4
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1.3k
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error using fitTimeSeries in metagenomeSeq
metagenomeseq fittimeseries
updated 7.5 years ago by ▴ 280 • written 7.5 years ago by • 0
0
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1
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1.0k
views
Understand fold changes
metagenomeseq
updated 7.6 years ago by ▴ 280 • written 7.6 years ago by ▴ 860
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6
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2.5k
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paired analysis using metagenomeSeq
metagenomeseq logfc paired samples standard error
updated 21 months ago by • 0 • written 7.6 years ago by ▴ 30
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5
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3.5k
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DESeq2 16s microbiome size factors
deseq2 metagenomeseq rnaseq 16s microbiome
updated 7.6 years ago by ▴ 280 • written 7.7 years ago by • 0
2
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1
reply
1.6k
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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
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1
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917
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fitTimeSeries possible error
metagenomeseq fittimeseries
updated 7.7 years ago by ▴ 280 • written 7.7 years ago by • 0
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2
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1.4k
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metagenomeSeq for continuous phenotype
metagenomeseq continuous limma
7.8 years ago pjgalli2 • 0
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1
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1.7k
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fitZig coefficient for interaction terms?
metagenomeseq
updated 7.9 years ago by ▴ 280 • written 7.9 years ago by • 0
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1
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1.0k
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Aggregate By Taxonomy Error
metagenomeSeq
updated 7.9 years ago by ▴ 280 • written 7.9 years ago by • 0
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5
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1.8k
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MetagenomSeq, perform anova or kruskall wallis with three groups ?
metagenomeseq anova metagenomics
8.0 years ago David ▴ 860
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3
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1.6k
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Normalisation problem in metagenomeSeq
normalization metagenomeseq
updated 8.0 years ago by ▴ 280 • written 8.0 years ago by ▴ 20
1
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1
reply
1.2k
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Multiple variables in fitFeaturemodel
metagenomeseq
updated 8.2 years ago by ▴ 280 • written 8.2 years ago by • 0
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0
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1.4k
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Dramatically different results from comparing multiple groups using fitZig versus fitFeatureModel
metagenomeseq
8.2 years ago craemuletz • 0
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0
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982
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Differential abundance for elevational gradient survey -- use fitTimeSeries?
metagenomeseq
8.2 years ago craemuletz • 0
3
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5
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2.5k
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Interpretation for MRfulltable of fitzig in Metagenomeseq
metagenomeseq fitzig MRfulltable
updated 8.2 years ago by ▴ 280 • written 8.2 years ago by • 0
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6
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3.2k
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Alpha diversity on Rlogtransformed data
deseq2 phyloseq metagenomeseq
8.4 years ago David ▴ 860
1
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1
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1.2k
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metagenomeSeq - normFactors
metagenomeseq
updated 8.5 years ago by ▴ 280 • written 8.5 years ago by ▴ 120
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4
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1.7k
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creating a subsetted MRexperiment based on sample name?
metagenomeseq
updated 8.7 years ago by ▴ 280 • written 8.7 years ago by • 0
4
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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
0
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7
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1.9k
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metagenomeSeq cumNorm issue with NAs in real data
metagenomeseq
updated 9.0 years ago by ▴ 280 • written 9.0 years ago by • 0
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1
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1.2k
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Metagenomeseq package; time series analysis
metagenomeseq software error
updated 9.1 years ago by ▴ 280 • written 9.1 years ago by • 0
1
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1
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1.4k
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Omission of final edge in correlationTest
metagenomeseq error correlationTest metagenomeseq
9.2 years ago eertel • 0
2
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4
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2.3k
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normFactors when aggregating in metagenomeSeq
metagenomeSeq microbiome
updated 16 months ago by • 0 • written 9.2 years ago by ▴ 30
1
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1
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3.0k
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Low quantile estimate using CSS normalization in metagenomeSeq
metagenomeSeq microbiome
updated 9.3 years ago by ▴ 280 • written 9.3 years ago by ▴ 30
1
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1
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1.6k
views
Problem reproducing metagenomeSeq tutorial example
metagenome microbiome metagenomeseq
updated 9.3 years ago by ▴ 280 • written 9.3 years ago by ▴ 30
2
votes
2
replies
1.3k
views
no timeInterval output using fitTimeSeries
metagenomeSeq fitTimeSeries microbiome
9.3 years ago noelle.noyes ▴ 30
50 results • Page 1 of 1
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Answer: DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR) by Michael Love 41k
> I got many p values that had "1.000000e+00" and padj "1" and stat of "0" when I added the Log threshold of LFC >1 and LFC < -1...is this …
Comment: Trying to use enrichGO by fernanda.backsouza ▴ 10
With all my love, thank you Guido, GOxploreR beeing a big ally for me. I don't know how to be grateful right now.
Comment: DESeq2 output used for PCA plot on R studio by swbarnes2 ★ 1.3k
You didn't generate it with an experiment, you made it up: Your PCA doesn't look like a good RNASeq experiment, because it's not.
Answer: Opposite sign of LFC in count plots of DEGs (DESeq2) by swbarnes2 ★ 1.3k
Your contrast is comparing LGR5 to Homeostasis. The bottom 2 are fine, it's the top one that is wrong. Are you sure this step isn't misla…
Comment: get BM error by James W. MacDonald 65k
I believe you need NCBI Gene IDs for KEGG, in which case you may need to map. The three genes you have shown here don't map, and of those t…
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Answer: How to retrieve gene ontology GO class from gene list?
Answer: How to retrieve gene ontology GO class from gene list?
C: when to apply quantile normalization with voom in limma/voom framework with RNA-
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A: Weird results (ribosomal proteins / Y-linked genes) in limma/voom
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