Showing : metagenomeSeq • reset
1
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4
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1.4k
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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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6
replies
3.2k
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Alpha diversity on Rlogtransformed data
deseq2 phyloseq metagenomeseq
8.4 years ago David ▴ 860
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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
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
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
0
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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
2
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2
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1.5k
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error using fitTimeSeries from metagenomeSeq
metagenomeSeq microbiome
9.3 years ago noelle.noyes ▴ 30
2
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2
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1.3k
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no timeInterval output using fitTimeSeries
metagenomeSeq fitTimeSeries microbiome
9.3 years ago noelle.noyes ▴ 30
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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
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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
1
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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
0
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5
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3.5k
views
DESeq2 16s microbiome size factors
deseq2 metagenomeseq rnaseq 16s microbiome
updated 7.7 years ago by ▴ 280 • written 7.7 years ago by • 0
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
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
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
2
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1
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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
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
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
0
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1
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1.4k
views
error on heatmap
PROMISE metagenomeSeq PROMISE metagenomeSeq
updated 10.1 years ago by ▴ 280 • written 10.1 years ago by ★ 13k
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1
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1.5k
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mouseData in heatmap of metagenomeSeq package
Metagenomics metagenomeSeq Metagenomics metagenomeSeq
updated 10.1 years ago by ▴ 280 • written 10.1 years ago by ★ 13k
2
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1
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2.5k
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metagenomeSeq error using cumNormStatFast
metagenomeSeq
updated 9.3 years ago by ▴ 280 • written 9.3 years ago by ▴ 30
1
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1
reply
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
1
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1
reply
3.0k
views
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
reply
1.2k
views
Metagenomeseq package; time series analysis
metagenomeseq software error
updated 9.1 years ago by ▴ 280 • written 9.1 years ago by • 0
4
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6
replies
1.5k
views
MetagenomeSeq sparsefeature question
metagenomeseq sparsefeature cumnorm
updated 8.8 years ago by 65k • written 8.8 years ago by • 0
1
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1
reply
1.2k
views
metagenomeSeq - normFactors
metagenomeseq
updated 8.5 years ago by ▴ 280 • written 8.5 years ago by ▴ 120
3
votes
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
1
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1
reply
1.2k
views
Multiple variables in fitFeaturemodel
metagenomeseq
updated 8.2 years ago by ▴ 280 • written 8.2 years ago by • 0
0
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3
replies
1.6k
views
Normalisation problem in metagenomeSeq
normalization metagenomeseq
updated 8.0 years ago by ▴ 280 • written 8.0 years ago by ▴ 20
0
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1
reply
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
0
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1
reply
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
0
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1
reply
917
views
fitTimeSeries possible error
metagenomeseq fittimeseries
updated 7.7 years ago by ▴ 280 • written 7.7 years ago by • 0
0
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1
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1.2k
views
MetagenomeSeq: analysing paired samples
metagenomeseq paired samples microbiome
updated 4.1 years ago by • 0 • written 7.4 years ago by • 0
0
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2
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1.4k
views
MetagenomeSeq: Sorting by sample type in plotMRheatmap
metagenomeSeq plotMRheatmap
updated 7.3 years ago by ▴ 280 • written 7.3 years ago by • 0
0
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6
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1.8k
views
metagenomeSeq log transformation
metagenomeseq logtransformation
updated 7.3 years ago by ▴ 280 • written 7.3 years ago by • 0
0
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1
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1.2k
views
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
0
votes
2
replies
1.1k
views
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
0
votes
1
reply
1.1k
views
metagenomeSeq: role for fitLogNormal?
metagenomeseq
updated 7.1 years ago by ▴ 280 • written 7.1 years ago by ▴ 10
1
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1
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1.7k
views
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
0
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1
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994
views
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
1
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1
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1.1k
views
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
0
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1
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816
views
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
0
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0
replies
631
views
Using MetagenomeSeq with intercept gives high logFC
limma metagenomeSeq
2.8 years ago edissepo • 0
0
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0
replies
951
views
Pattern Search in MicrobiomeAnalyst
metagenomeSeq Metagenomics microbiome microbiomeExplorer
2.8 years ago GlycineMax • 0
0
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10
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1.9k
views
Phyloseq to metagenomeSeq
limma metagenomeSeq
4.9 years ago Jitendra ▴ 10
0
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0
replies
982
views
Differential abundance for elevational gradient survey -- use fitTimeSeries?
metagenomeseq
8.2 years ago craemuletz • 0
0
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0
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968
views
Paired Difference Analysis
metagenomeseq
6.2 years ago nhua • 0
0
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1
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1.4k
views
[metagenomeSeq] "Error: Warning sample with one or zero features" from cumNormStatFast
metagenomeseq cumNormStatFast features error
5.9 years ago jol.espinoz ▴ 40
0
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1
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1.1k
views
metagenomeSeq error question: error on creation of newMRexperiment
metagenomeseq error metagenomeseq microbiome
5.4 years ago slizo001 • 0
0
votes
0
replies
890
views
Including covariates with fitFeatureModel
metagenomeSeq
4.5 years ago dkorandla • 0
50 results • Page 1 of 1
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Comment: Reproducibility issue with scran together with lapply and BiocParallel by ATpoint ★ 4.0k
Thanks Aaron for the response. RNGseed (for me) has no effect. I actually stumbled over this in one of my analysis where I have a constant …
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2) by winwater0928 • 0
Thank you for your comment! 1)"Your contrast is comparing LGR5 to Homeostasis." means (Lgr5)/(Homeostasis). Is it right? Then, I think if…
Answer: Reproducibility issue with scran together with lapply and BiocParallel by Aaron Lun ★ 28k
IIRC **BiocParallel** switches to a different RNG when inside its own functions like `bplapply` - specifically L'Ecuyer-CMRG, as opposed to…
Comment: DESeq2 output used for PCA plot on R studio by swbarnes2 ★ 1.3k
This looks terrible for RNASeq data, because it's not RNASeq data. It's a matrix of pretty random numbers, which you know because you poste…
Comment: DESeq2 output used for PCA plot on R studio by Aaliya • 0
I had taken this code from internet, but after reading about it and I did on my own, I would be making a post to ask for the suggestions if…
Votes
C: null model and DEXSeqDataSet object in DEXSEQ
A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
A: How to explain how DESeq2 works to someone with zero bioinformatics background?
Answer: Interpret plot from DiffBind
Answer: How to retrieve gene ontology GO class from gene list?
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