Showing : microbiome • reset
1
vote
3
replies
6.8k
views
DESeq2 - Error: full model matrix is less than full rank
microbiome DESeq2
updated 18 months ago by ▴ 30 • written 3.5 years ago by • 0
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 9.5 years ago by 41k • written 9.6 years ago by • 0
0
votes
5
replies
3.5k
views
DESeq2 16s microbiome size factors
deseq2 metagenomeseq rnaseq 16s microbiome
updated 7.6 years ago by ▴ 280 • written 7.6 years ago by • 0
1
vote
1
reply
3.5k
views
Normalization/Transformation Before Microbiome Alpha Diversity Analysis
microbiome normalization variancestabilizingtransformation phyloseq
7.0 years ago stats134711 • 0
0
votes
3
replies
3.3k
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 41k
3
votes
2
replies
3.3k
views
DESeq2 iterative size factor normalization did not converge
deseq2 microbiome phyloseq
updated 6.6 years ago by 41k • written 6.6 years ago by • 0
0
votes
8
replies
3.2k
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 10.4 years ago by 41k
6
votes
1
reply
3.2k
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 7.5 years ago by ★ 13k • written 7.5 years ago by ▴ 20
0
votes
0
replies
3.1k
views
Bioconductor 2.11 is released
BiocViews SNP Transcription Sequencing miRNA Microbiome Microarray qPCR Genetics Coverage
11.5 years ago Dan Tenenbaum ★ 8.2k
1
vote
1
reply
3.0k
views
Low quantile estimate using CSS normalization in metagenomeSeq
metagenomeSeq microbiome
updated 9.2 years ago by ▴ 280 • written 9.2 years ago by ▴ 30
2
votes
19
replies
2.9k
views
phyloseq/DESeq gives negative transformed values
Microbiome DESeq Microbiome DESeq
updated 10.0 years ago by 41k • written 10.0 years ago by ▴ 130
0
votes
0
replies
2.6k
views
Pathview with non-KEGG organisms?
Microbiome Pathways GO Visualization Organism graph gage pathview Microbiome Pathways GO
10.7 years ago Luo Weijun ★ 1.6k
2
votes
4
replies
2.3k
views
normFactors when aggregating in metagenomeSeq
metagenomeSeq microbiome
updated 16 months ago by • 0 • written 9.2 years ago by ▴ 30
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 41k • written 7.8 years ago by • 0
1
vote
2
replies
1.9k
views
Normalization factors in metagenomeSeq
microbiome
9.0 years ago jovel_juan ▴ 30
2
votes
1
reply
1.8k
views
Drastic DE result discrepancies between versions of DESeq2
deseq2 differential expression microbiome
updated 8.6 years ago by 41k • written 8.6 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 6.4 years ago by ▴ 280 • written 6.4 years ago by ▴ 10
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
0
votes
1
reply
1.6k
views
DeSeq2 for comparison of experimental factors on microbial composition
deseq2 microbiome fungi fungal microbiome
updated 5.9 years ago by 41k • written 5.9 years ago by • 0
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 7.0 years ago by ★ 13k • written 7.0 years ago by • 0
2
votes
1
reply
1.6k
views
Deseq2 for 16s Data
Microbiome 16s Deseq2 16srRNA
updated 24 months ago by 41k • written 24 months ago by ▴ 10
0
votes
3
replies
1.6k
views
I cannot install "microbiome"
GenomeInfoDbData microbiome phyloseq
updated 20 months ago by 690 • written 20 months ago by • 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 41k • written 3.6 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
6.8 years ago lanhuong ▴ 20
1
vote
1
reply
1.6k
views
Problem reproducing metagenomeSeq tutorial example
metagenome microbiome metagenomeseq
updated 9.2 years ago by ▴ 280 • written 9.2 years ago by ▴ 30
2
votes
2
replies
1.5k
views
error using fitTimeSeries from metagenomeSeq
metagenomeSeq microbiome
9.3 years ago noelle.noyes ▴ 30
0
votes
5
replies
1.5k
views
deseq2 analysis, accounting for pen effect
deseq2 microbiome
updated 8.4 years ago by ★ 13k • written 8.4 years ago by ▴ 10
0
votes
2
replies
1.5k
views
metagenomeSeq: cumNormStat normalization default
metagenomeseq microbiome
7.4 years ago Brian Smith ▴ 120
0
votes
2
replies
1.4k
views
DESeq2 Interaction Term Interpretation for Microbiome Data
deseq2 microbiome
updated 4.8 years ago by ★ 1.3k • written 4.8 years ago by • 0
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
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 41k • written 6.4 years ago by • 0
2
votes
2
replies
1.3k
views
no timeInterval output using fitTimeSeries
metagenomeSeq fitTimeSeries microbiome
9.3 years ago noelle.noyes ▴ 30
0
votes
0
replies
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
7.7 years ago Daniel Brewer ▴ 100
0
votes
2
replies
1.3k
views
DESeq2 error on analyzing microbiome data
deseq2 microbiome sequencing
4.8 years ago zhigang.li • 0
0
votes
2
replies
1.3k
views
stat_compare_means function - Error 'must have same length'
microbiomeDataSets Microbiome
14 months ago Elif • 0
0
votes
0
replies
1.3k
views
Job: EXTENDED: Bioinformatics Specialist at the University of Illinois
microbiome epigenomics bioinformatics analyst NGS Job
6.1 years ago Jenny Drnevich ★ 2.0k
0
votes
0
replies
1.3k
views
Job: Bioinformatics Specialist at the University of Illinois
job bioinformatics microbiome metagenomics epigenomics Job
6.2 years ago Jenny Drnevich ★ 2.0k
0
votes
1
reply
1.2k
views
error with fitTimeSeries in metagenomeSeq" invalid 'times’ argument"
microbiome
updated 9.4 years ago by ▴ 280 • written 9.4 years ago by • 0
0
votes
1
reply
1.2k
views
MetagenomeSeq: analysing paired samples
metagenomeseq paired samples microbiome
updated 4.0 years ago by • 0 • written 7.4 years ago by • 0
0
votes
2
replies
1.2k
views
Question: export edgeR normalised OTU table
microbiome edgeR
3.2 years ago Pozdrawiam • 0
0
votes
1
reply
1.1k
views
metagenomeSeq error question: error on creation of newMRexperiment
metagenomeseq error metagenomeseq microbiome
5.3 years ago slizo001 • 0
2
votes
1
reply
1.1k
views
Rsubread for microbiome data analysis: genome >4GB
alignment rsubread microbiome
updated 5.4 years ago by ★ 3.6k • written 5.4 years ago by ▴ 850
0
votes
1
reply
1.0k
views
Question about multi-factor Deseq analysis
DESeq deseq2 microbiome gut microbiome
updated 5.5 years ago by 41k • written 5.5 years ago by • 0
0
votes
0
replies
985
views
News: Early career researchers: nominate to present your work at BVCN virtual conference on microbiome research
microbiome news Conference
3.2 years ago Matthew Ritchie ▴ 1000
2
votes
1
reply
963
views
Software Compatibility Issue Between phyloseq and lme4 Packages
phyloseq microbiome Software
updated 7 months ago by ★ 4.0k • written 7 months ago by ▴ 10
0
votes
0
replies
939
views
Pattern Search in MicrobiomeAnalyst
metagenomeSeq Metagenomics microbiome microbiomeExplorer
2.8 years ago GlycineMax • 0
0
votes
0
replies
923
views
Job: Bioinformatician Positions at the University of Chicago BSD Bioinformatics Core
RNA-seq DNA-seq ATAC-seq proteomics microbiome Job
4.3 years ago lhuang7 ▴ 50
0
votes
0
replies
887
views
Aldex2 feature request - controlling for additional variables
ALDEx2 ALDEx microbiome 16s
5.3 years ago mstagliamonte ▴ 10
0
votes
1
reply
875
views
Editing Plots Generated Using MicrobiomeAnalyst
MicrobiomeData microbiome offtopic
updated 2.7 years ago by 65k • written 2.7 years ago by • 0
1
vote
0
replies
862
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
4.5 years ago supindab ▴ 10
50 results • Page 1 of 1
Recent ...
Replies
Comment: DESeq filtering specific to contrasts by Carlin95 • 0
But wouldn't this result in a different gene set for each analysis stratification? How can you then compare if maybe gene x comes up in Tim…
Comment: Reading huge bismark coverage files using bbseq::read.bismark by jacques.imbert • 0
Hello, Using nThread = 1L fixed the issue. Thank you for your time and help.
Comment: Error in champ.load(): The following specified files do not exist by Basti ▴ 760
The error stems from the Basename column, please see solution here : https://support.bioconductor.org/p/p132482/
Comment: FilterByExpr low counts with small sample size by Gordon Smyth 50k
As always, it helps to see code. Are you running `voom` or `voomLmFit`? Did you run `normLibSizes()` in edgeR prior to `voom`? Are you star…
Comment: Batch correction and repeated measures by Gordon Smyth 50k
In your code, it was clear that `expr.mat` was a matrix rather than a DGEList, so it has to be a count matrix. If you have a DGEList object…
Votes
Comment: Reading huge bismark coverage files using bbseq::read.bismark
Answer: Reading huge bismark coverage files using bbseq::read.bismark
Answer: Reading huge bismark coverage files using bbseq::read.bismark
Answer: How many of my genes from my gene list are in each KEGG pathway?
Comment: Light difference when using coef vs omit a group when compare 3 groups.
Awards • All
Popular Question to paria.alipour • 0
Popular Question to Eman • 0
Popular Question to James W. MacDonald 65k
Scholar to nhaus ▴ 30
Popular Question to shepherl 3.8k
Locations • All
France, just now
WEHI, Melbourne, Australia, 7 minutes ago
Germany, 18 minutes ago
Germany, 36 minutes ago
Estonia, 50 minutes ago
Traffic: 823 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6