Showing : microbiome • reset
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DESeq2 - Error: full model matrix is less than full rank
microbiome DESeq2
updated 19 months ago by ▴ 30 • written 3.6 years ago by • 0
1
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2
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4.6k
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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
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5
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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
1
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1
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3.5k
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Normalization/Transformation Before Microbiome Alpha Diversity Analysis
microbiome normalization variancestabilizingtransformation phyloseq
7.1 years ago stats134711 • 0
0
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3
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3.4k
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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
3
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2
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3.4k
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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
0
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8
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3.3k
views
Variance stabilizing transformation seems not working on NGS (bacterial 16srRNA based) data
Microbiome DESeq2 Microbiome DESeq2
updated 7.8 years ago by ★ 13k • written 10.5 years ago by 42k
6
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1
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3.3k
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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
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0
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3.1k
views
Bioconductor 2.11 is released
BiocViews SNP Transcription Sequencing miRNA Microbiome Microarray qPCR Genetics Coverage
11.6 years ago Dan Tenenbaum ★ 8.2k
1
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1
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3.1k
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
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19
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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
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0
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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
2
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4
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2.3k
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normFactors when aggregating in metagenomeSeq
metagenomeSeq microbiome
updated 17 months ago by • 0 • written 9.3 years ago by ▴ 30
4
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3
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2.0k
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Analyzing microbiome data (many zero-counts) using DESeq2
DESeq2 microbiome zero-inflated
updated 7.9 years ago by 42k • written 7.9 years ago by • 0
1
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2
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1.9k
views
Normalization factors in metagenomeSeq
microbiome
9.1 years ago jovel_juan ▴ 30
2
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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
1
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1
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1.8k
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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
2
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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
1
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1
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1.7k
views
metagenomeSeq error using plotMRheatmap and display() heatmaps and PCA/MDS plots
metagenomseq microbiome
updated 9.4 years ago by ▴ 280 • written 9.4 years ago by ▴ 30
0
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3
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1.7k
views
I cannot install "microbiome"
GenomeInfoDbData microbiome phyloseq
updated 21 months ago by 700 • written 21 months ago by • 0
0
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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
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3
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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
2
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1.6k
views
Differential Abundance Analysis wih DESeq2 and metabolites as continuous predictor variables
deseq2 microbiome R
updated 3.7 years ago by 42k • written 3.7 years ago by • 0
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
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
0
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5
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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
2
votes
2
replies
1.6k
views
error using fitTimeSeries from metagenomeSeq
metagenomeSeq microbiome
9.4 years ago noelle.noyes ▴ 30
0
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2
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1.5k
views
metagenomeSeq: cumNormStat normalization default
metagenomeseq microbiome
7.5 years ago Brian Smith ▴ 120
0
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2
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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
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3
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1.4k
views
Correlation analysis
Microbiome HIV Microbiome HIV
updated 12.5 years ago by 21k • written 12.5 years ago by ▴ 20
1
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1
reply
1.4k
views
Getting OTUID rather than Taxonomy from Results function in DESeq2
deseq2 R microbiome phyloseq qiime
updated 6.5 years ago by 42k • written 6.5 years ago by • 0
0
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2
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1.4k
views
stat_compare_means function - Error 'must have same length'
microbiomeDataSets Microbiome
15 months ago Elif • 0
2
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2
replies
1.3k
views
no timeInterval output using fitTimeSeries
metagenomeSeq fitTimeSeries microbiome
9.4 years ago noelle.noyes ▴ 30
0
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0
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1.3k
views
Job: 2 year bioinformatics postdoc in the microbiome and prostate cancer risk @ UEA, Norwich, UK
Cancer microbiome postdoc UK prostate cancer Job
7.8 years ago Daniel Brewer ▴ 100
0
votes
2
replies
1.3k
views
DESeq2 error on analyzing microbiome data
deseq2 microbiome sequencing
4.9 years ago zhigang.li • 0
0
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0
replies
1.3k
views
Job: EXTENDED: Bioinformatics Specialist at the University of Illinois
microbiome epigenomics bioinformatics analyst NGS Job
6.2 years ago Jenny Drnevich ★ 2.0k
0
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0
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1.3k
views
Job: Bioinformatics Specialist at the University of Illinois
job bioinformatics microbiome metagenomics epigenomics Job
6.3 years ago Jenny Drnevich ★ 2.0k
0
votes
1
reply
1.3k
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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1
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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
0
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2
replies
1.2k
views
Question: export edgeR normalised OTU table
microbiome edgeR
3.3 years ago Pozdrawiam • 0
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
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
2
votes
1
reply
1.1k
views
Software Compatibility Issue Between phyloseq and lme4 Packages
phyloseq microbiome Software
updated 8 months ago by ★ 4.1k • written 8 months ago by ▴ 10
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
0
votes
0
replies
1.0k
views
News: Early career researchers: nominate to present your work at BVCN virtual conference on microbiome research
microbiome news Conference
3.3 years ago Matthew Ritchie ▴ 1000
0
votes
0
replies
982
views
Pattern Search in MicrobiomeAnalyst
metagenomeSeq Metagenomics microbiome microbiomeExplorer
2.9 years ago GlycineMax • 0
0
votes
0
replies
951
views
Job: Bioinformatician Positions at the University of Chicago BSD Bioinformatics Core
RNA-seq DNA-seq ATAC-seq proteomics microbiome Job
4.4 years ago lhuang7 ▴ 50
0
votes
1
reply
922
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
0
replies
918
views
Aldex2 feature request - controlling for additional variables
ALDEx2 ALDEx microbiome 16s
5.4 years ago mstagliamonte ▴ 10
1
vote
0
replies
892
views
Job: Bioinformatician: NEW YORK CITY - Institute for Data Science and Genomic Technology, Mount Sinai School of Medicine
job bioinformatician systems biology microbiome genomics Job
4.6 years ago supindab ▴ 10
50 results • Page 1 of 1
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Comment: all variables in design formula must be columns in colData (Deseq2) error by Galina • 0
thank you!
Comment: all variables in design formula must be columns in colData (Deseq2) error by ATpoint ★ 4.1k
coldata_rat <- data.frame(conditions=..., batch=...)
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it by robersy • 0
Thank you all for your comments. I will follow your suggestions.
Comment: Numerical differences in DESeq2 output depending on different design matrix cons by Ken C • 0
Hi Michael, thanks a lot for your prompt reply! Not sure if this is appropriate or if you are the right person to ask -- is there anything…
Comment: Numerical differences in DESeq2 output depending on different design matrix cons by Ken C • 0
Well, if I look at genes with baseMean>50, then the relative absolute difference in log2FoldChange (say over the absolute log2FoldChange of…
Votes
biomaRt not working - lazy table error
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Comment: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Comment: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
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