Showing : metagenomeseq • reset
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
0
votes
7
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1.9k
views
metagenomeSeq cumNorm issue with NAs in real data
metagenomeseq
updated 9.0 years ago by ▴ 280 • written 9.0 years ago by • 0
4
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6
replies
1.5k
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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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6
replies
3.2k
views
Alpha diversity on Rlogtransformed data
deseq2 phyloseq metagenomeseq
8.4 years ago David ▴ 860
0
votes
6
replies
2.5k
views
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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6
replies
4.1k
views
Difference between fitFeatureModel and fitZIG in metagenomeSeq
metagenomeseq
7.1 years ago sasha • 0
0
votes
6
replies
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
0
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5
replies
1.8k
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MetagenomSeq, perform anova or kruskall wallis with three groups ?
metagenomeseq anova metagenomics
8.0 years ago David ▴ 860
0
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5
replies
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
3
votes
5
replies
2.5k
views
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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4
replies
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
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
1
vote
4
replies
1.4k
views
error using fitTimeSeries in metagenomeSeq
metagenomeseq fittimeseries
updated 7.5 years ago by ▴ 280 • written 7.6 years ago by • 0
0
votes
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
votes
2
replies
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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2
replies
1.5k
views
metagenomeSeq: cumNormStat normalization default
metagenomeseq microbiome
7.4 years ago Brian Smith ▴ 120
0
votes
2
replies
1.1k
views
Filter low counts OTUs from a MRfull table to prepare a heatmap
metagenomeseq
6.2 years ago arguello.rguez • 0
2
votes
2
replies
1.5k
views
error using fitTimeSeries from metagenomeSeq
metagenomeSeq microbiome
9.3 years ago noelle.noyes ▴ 30
0
votes
2
replies
1.3k
views
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
1
vote
2
replies
1.4k
views
metagenomeSeq for continuous phenotype
metagenomeseq continuous limma
7.8 years ago pjgalli2 • 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
2
votes
2
replies
1.3k
views
no timeInterval output using fitTimeSeries
metagenomeSeq fitTimeSeries microbiome
9.3 years ago noelle.noyes ▴ 30
1
vote
1
reply
1.4k
views
Omission of final edge in correlationTest
metagenomeseq error correlationTest metagenomeseq
9.2 years ago eertel • 0
0
votes
1
reply
1.4k
views
error on heatmap
PROMISE metagenomeSeq PROMISE metagenomeSeq
updated 10.1 years ago by ▴ 280 • written 10.1 years ago by ★ 13k
0
votes
1
reply
1.5k
views
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
votes
1
reply
2.5k
views
metagenomeSeq error using cumNormStatFast
metagenomeSeq
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
1
vote
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
1
vote
1
reply
1.2k
views
metagenomeSeq - normFactors
metagenomeseq
updated 8.5 years ago by ▴ 280 • written 8.5 years ago by ▴ 120
1
vote
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
votes
1
reply
1.0k
views
Aggregate By Taxonomy Error
metagenomeSeq
updated 7.9 years ago by ▴ 280 • written 7.9 years ago by • 0
0
votes
1
reply
1.7k
views
fitZig coefficient for interaction terms?
metagenomeseq
updated 7.9 years ago by ▴ 280 • written 7.9 years ago by • 0
0
votes
1
reply
918
views
fitTimeSeries possible error
metagenomeseq fittimeseries
updated 7.7 years ago by ▴ 280 • written 7.7 years ago by • 0
2
votes
1
reply
1.6k
views
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
votes
1
reply
1.0k
views
Understand fold changes
metagenomeseq
updated 7.6 years ago by ▴ 280 • written 7.6 years ago by ▴ 860
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
0
votes
1
reply
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
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
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
0
votes
1
reply
997
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
reply
1.2k
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
reply
1.4k
views
[metagenomeSeq] "Error: Warning sample with one or zero features" from cumNormStatFast
metagenomeseq cumNormStatFast features error
6.0 years ago jol.espinoz ▴ 40
0
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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
820
views
Tool for metagenomic functional analysis with 4-factor study design
Metagenomics DESeq2 metagenomeSeq edgeR KEGG
updated 2.1 years ago by 41k • written 2.1 years ago by • 0
0
votes
0
replies
969
views
Paired Difference Analysis
metagenomeseq
6.2 years ago nhua • 0
0
votes
0
replies
632
views
Using MetagenomeSeq with intercept gives high logFC
limma metagenomeSeq
2.8 years ago edissepo • 0
0
votes
0
replies
953
views
Pattern Search in MicrobiomeAnalyst
metagenomeSeq Metagenomics microbiome microbiomeExplorer
2.8 years ago GlycineMax • 0
0
votes
0
replies
984
views
Differential abundance for elevational gradient survey -- use fitTimeSeries?
metagenomeseq
8.2 years ago craemuletz • 0
0
votes
0
replies
891
views
Including covariates with fitFeatureModel
metagenomeSeq
4.5 years ago dkorandla • 0
50 results • Page 1 of 1
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Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length by ussarizona ▴ 10
Hi Michael, Yes, I could figure it out what does the error mean. In my matrix I had the first colum GeneID while in my condition I only h…
Answer: Deseq2. decontXcounts not integers. Useful alternative? by Michael Love 41k
Another option would be to put the per sample estimated contamination in the design. This is for example how RUV etc help remove spurious D…
Answer: ATACseq merge peaks by ATpoint ★ 4.0k
That depends on your analysis. Typically, for differential analysis (and convenience) you would produce a single set of peaks (e.g. by merg…
Comment: Deseq2. decontXcounts not integers. Useful alternative? by camp ▴ 10
Yes, @atpoint is correct. decontX decontaminated counts are not integers due to the way the variation inference algorithm works, but you ca…
Comment: Deseq2. decontXcounts not integers. Useful alternative? by ATpoint ★ 4.0k
I do not know this decontamination tool you use but generally: If these counts are basically "corrected" raw counts in the sense that they'…
Votes
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
Comment: Deseq2. decontXcounts not integers. Useful alternative?
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
biomaRt error: database disk image is malformed
Comment: biomaRt : No lock file for BiocFileCache
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