Showing : microbiome • reset
2
votes
19
replies
2.9k
views
phyloseq/DESeq gives negative transformed values
Microbiome DESeq Microbiome DESeq
updated 10.1 years ago by 42k • written 10.1 years ago by ▴ 130
0
votes
8
replies
3.3k
views
Variance stabilizing transformation seems not working on NGS (bacterial 16srRNA based) data
Microbiome DESeq2 Microbiome DESeq2
updated 7.7 years ago by ★ 13k • written 10.5 years ago by 42k
0
votes
6
replies
1.6k
views
Why DESeq2 gives large logfold for group with all zero count?
microbiome 16s deseq2 differential gene expression
6.9 years ago lanhuong ▴ 20
0
votes
5
replies
1.6k
views
deseq2 analysis, accounting for pen effect
deseq2 microbiome
updated 8.5 years ago by ★ 13k • written 8.5 years ago by ▴ 10
0
votes
5
replies
3.6k
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
2
votes
4
replies
2.3k
views
normFactors when aggregating in metagenomeSeq
metagenomeSeq microbiome
updated 17 months ago by • 0 • written 9.2 years ago by ▴ 30
0
votes
3
replies
1.6k
views
Where to find open access microbiome data for case-control comparative study?
microbiome data analysis data request
updated 7.1 years ago by ★ 13k • written 7.1 years ago by • 0
0
votes
3
replies
1.6k
views
I cannot install "microbiome"
GenomeInfoDbData microbiome phyloseq
updated 21 months ago by 690 • written 21 months ago by • 0
4
votes
3
replies
2.0k
views
Analyzing microbiome data (many zero-counts) using DESeq2
DESeq2 microbiome zero-inflated
updated 7.8 years ago by 42k • written 7.8 years ago by • 0
1
vote
3
replies
6.9k
views
DESeq2 - Error: full model matrix is less than full rank
microbiome DESeq2
updated 19 months ago by ▴ 30 • written 3.5 years ago by • 0
0
votes
3
replies
3.4k
views
phyloseq/DESeq gives negative transformed values
Microbiome Normalization Clustering DESeq DESeq2 Microbiome Normalization Clustering DESeq
updated 10.0 years ago by ▴ 130 • written 10.0 years ago by 42k
0
votes
3
replies
1.4k
views
Correlation analysis
Microbiome HIV Microbiome HIV
updated 12.5 years ago by 21k • written 12.5 years ago by ▴ 20
1
vote
2
replies
4.6k
views
DESeq2: What is the impact if glm.fit does not converge during rlogTransformation or varianceStabilizingTransformation
deseq2 normalization microbiome
updated 9.6 years ago by 42k • written 9.6 years ago by • 0
0
votes
2
replies
1.3k
views
DESeq2 error on analyzing microbiome data
deseq2 microbiome sequencing
4.8 years ago zhigang.li • 0
3
votes
2
replies
3.3k
views
DESeq2 iterative size factor normalization did not converge
deseq2 microbiome phyloseq
updated 6.7 years ago by 42k • written 6.7 years ago by • 0
2
votes
2
replies
1.6k
views
error using fitTimeSeries from metagenomeSeq
metagenomeSeq microbiome
9.3 years ago noelle.noyes ▴ 30
2
votes
2
replies
1.3k
views
no timeInterval output using fitTimeSeries
metagenomeSeq fitTimeSeries microbiome
9.3 years ago noelle.noyes ▴ 30
0
votes
2
replies
1.4k
views
stat_compare_means function - Error 'must have same length'
microbiomeDataSets Microbiome
15 months ago Elif • 0
0
votes
2
replies
1.6k
views
Differential Abundance Analysis wih DESeq2 and metabolites as continuous predictor variables
deseq2 microbiome R
updated 3.6 years ago by 42k • written 3.6 years ago by • 0
0
votes
2
replies
1.5k
views
DESeq2 Interaction Term Interpretation for Microbiome Data
deseq2 microbiome
updated 4.9 years ago by ★ 1.4k • written 4.9 years ago by • 0
0
votes
2
replies
1.2k
views
Question: export edgeR normalised OTU table
microbiome edgeR
3.3 years ago Pozdrawiam • 0
0
votes
2
replies
852
views
DESeq2: seeking advice regarding before/after mutliple treatements + extra factor
deseq2 16s microbiome
updated 4.3 years ago by 42k • written 4.3 years ago by ▴ 10
1
vote
2
replies
1.9k
views
Normalization factors in metagenomeSeq
microbiome
9.1 years ago jovel_juan ▴ 30
0
votes
2
replies
500
views
DESeq2 for microbiome data: raw counts or percentages?
microbiome DESeq2
5 months ago anton.kratz ▴ 60
0
votes
2
replies
1.5k
views
metagenomeSeq: cumNormStat normalization default
metagenomeseq microbiome
7.5 years ago Brian Smith ▴ 120
1
vote
1
reply
3.5k
views
Normalization/Transformation Before Microbiome Alpha Diversity Analysis
microbiome normalization variancestabilizingtransformation phyloseq
7.1 years ago stats134711 • 0
0
votes
1
reply
1.2k
views
error with fitTimeSeries in metagenomeSeq" invalid 'times’ argument"
microbiome
updated 9.5 years ago by ▴ 280 • written 9.5 years ago by • 0
1
vote
1
reply
1.7k
views
metagenomeSeq error using plotMRheatmap and display() heatmaps and PCA/MDS plots
metagenomseq microbiome
updated 9.3 years ago by ▴ 280 • written 9.3 years ago by ▴ 30
1
vote
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
vote
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
2
votes
1
reply
1.8k
views
Drastic DE result discrepancies between versions of DESeq2
deseq2 differential expression microbiome
updated 8.7 years ago by 42k • written 8.7 years ago by • 0
6
votes
1
reply
3.3k
views
Using R package 'limma' on pre-normalized counts and the effect of non-equivalent reads/sample on limma linear model
limma rna-seq multi-mapped reads normalization microbiome
updated 7.6 years ago by ★ 13k • written 7.6 years ago by ▴ 20
0
votes
1
reply
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
1
vote
1
reply
1.7k
views
Should I normalize communities separately with metagenomeseq?
metagenomeseq microbiome gut microbiome metagenomics shotgun metagenomics
updated 6.5 years ago by ▴ 280 • written 6.5 years ago by ▴ 10
1
vote
1
reply
1.4k
views
Getting OTUID rather than Taxonomy from Results function in DESeq2
deseq2 R microbiome phyloseq qiime
updated 6.4 years ago by 42k • written 6.4 years ago by • 0
0
votes
1
reply
1.6k
views
DeSeq2 for comparison of experimental factors on microbial composition
deseq2 microbiome fungi fungal microbiome
updated 6.0 years ago by 42k • written 6.0 years ago by • 0
0
votes
1
reply
1.0k
views
Question about multi-factor Deseq analysis
DESeq deseq2 microbiome gut microbiome
updated 5.5 years ago by 42k • written 5.5 years ago by • 0
2
votes
1
reply
1.1k
views
Rsubread for microbiome data analysis: genome >4GB
alignment rsubread microbiome
updated 5.5 years ago by ★ 3.6k • written 5.5 years ago by ▴ 850
0
votes
1
reply
1.1k
views
metagenomeSeq error question: error on creation of newMRexperiment
metagenomeseq error metagenomeseq microbiome
5.4 years ago slizo001 • 0
0
votes
1
reply
712
views
Query regarding phyloseq object construct with QIIME output
phyloseq microbiome Metagenomics
updated 27 days ago by • 0 • written 11 months ago by • 0
2
votes
1
reply
1.7k
views
Deseq2 for 16s Data
Microbiome 16s Deseq2 16srRNA
updated 2.1 years ago by 42k • written 2.1 years ago by ▴ 10
0
votes
1
reply
910
views
Editing Plots Generated Using MicrobiomeAnalyst
MicrobiomeData microbiome offtopic
updated 2.8 years ago by 65k • written 2.8 years ago by • 0
0
votes
1
reply
804
views
DESeq2 differences in Wald and LRT in multi-factorial design
microbiome LRT DESeq2
updated 2.3 years ago by 42k • written 2.3 years ago by • 0
0
votes
1
reply
581
views
pairwise within sample
DESeq2 microbiome
updated 2.7 years ago by 42k • written 2.7 years ago by • 0
2
votes
1
reply
1.0k
views
Software Compatibility Issue Between phyloseq and lme4 Packages
phyloseq microbiome Software
updated 7 months ago by ★ 4.1k • written 7 months ago by ▴ 10
0
votes
1
reply
691
views
How to add rowLinks, rowTree in SummarizedExperiment manually.
TreeSummarizedExperiment phylogenetic microbiome SummarizedExperiment
updated 20 months ago by 65k • written 20 months ago by • 0
0
votes
1
reply
882
views
Adding insect abundance data to SparCC Analysis
sparcc Microbiome microbiomeExplorer MicrobiomeData
updated 2.9 years ago by ★ 3.9k • written 2.9 years ago by • 0
1
vote
1
reply
138
views
Dominance Index for Shotgun Metagenomics Data
microbiome
updated 13 days ago by ▴ 40 • written 14 days ago by ★ 1.5k
0
votes
0
replies
972
views
Pattern Search in MicrobiomeAnalyst
metagenomeSeq Metagenomics microbiome microbiomeExplorer
2.9 years ago GlycineMax • 0
0
votes
0
replies
2.6k
views
Pathview with non-KEGG organisms?
Microbiome Pathways GO Visualization Organism graph gage pathview Microbiome Pathways GO
10.8 years ago Luo Weijun ★ 1.6k
50 results • Page 1 of 1
Recent ...
Replies
Comment: Extremely small p-values using Limma for proteomic data by James W. MacDonald 65k
If you ever find yourself using the `@` function, you should reconsider what you are doing. There are vanishingly small instances when an e…
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Michael Love 42k
Here is some example code <https://gist.github.com/mikelove/cbbc84634b6854c865cb5eb08ad9b245>
Comment: How to use spike-in information (sequences from another species) with DESeq2::DE by maria.soler • 0
Hi, I have a question barely related to this topic. Do you use a custom reference genome combining your organism and the one used as a spik…
Answer: Differential gene expression analysis results by ATpoint ★ 4.1k
Pease do not open multiple posts for the same issue: https://support.bioconductor.org/p/9158194/#9158222 The support site is not meant f…
Comment: deseq2 results by sajadahmad41454 • 0
thank you for your response, should i remove or discard that sample? since the red outlier on left represents one of healthy samples.
Votes
A: AIC-like measure for DESeq2
Comment: Extremely small p-values using Limma for proteomic data
Comment: Log-cpm values from limma
Comment: Log-cpm values from limma
Comment: deseq2 results
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