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outliers
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Which samples to remove from analysis based on Cook's distance outliers plot
DESeq2
cooks
outliers
updated 12 months ago by
ATpoint
★ 4.0k • written 12 months ago by
Michael
• 0
0
votes
3
replies
932
views
dealing with outliers (deseq2)
maxcooks
outliers
zero
counts
DESeq2
updated 2.0 years ago by
Michael Love
41k • written 2.0 years ago by
andreia
▴ 10
1
vote
2
replies
990
views
rlog vs vst for outlier identification
rlog
DESeq2
vst
outliers
2.2 years ago
Bex
• 0
8
votes
2
replies
6.5k
views
handling outliers with DESeq2
RNASeqData
DESeq2
Outliers
2.9 years ago
paty
▴ 60
0
votes
2
replies
701
views
Outliers
outliers
Deseq2
3.0 years ago
nolwenn
• 0
7
votes
8
replies
2.0k
views
Cook's Distance Outliers: None reported in results table and "cooksCutoff" modification has no effect
deseq2
outliers
cooks
cooks distance
updated 3.6 years ago by
Michael Love
41k • written 3.6 years ago by
donnenfieldjonah
• 0
2
votes
3
replies
1.8k
views
DESeq2 count outlier replacement from Cook's threshold
deseq2
deseq
rnaseq
outliers
count outliers
updated 5.3 years ago by
Michael Love
41k • written 5.3 years ago by
lefeverde
▴ 10
1
vote
7
replies
1.6k
views
skewed differentially expressed gene results - DESeq2
deseq2
differential gene expression
outliers
updated 5.7 years ago by
Ryan C. Thompson
★ 7.9k • written 5.7 years ago by
CE
▴ 20
0
votes
1
reply
1.3k
views
Deseq2 default Cooks distance threshold
Deseq2
outliers
cookscutoff
updated 5.7 years ago by
Michael Love
41k • written 5.7 years ago by
jaime.alvarez.benayas
• 0
1
vote
2
replies
1.1k
views
Odd Sample after SWAN normalisation, DNA methylation analysis EPIC array
minfi
normalization
outliers
dna methylation
densityplot
5.7 years ago
peter.fransquet
• 0
0
votes
1
reply
818
views
Removal of outliers after library size correction, can I save this to my dds object?
deseq2
outliers
updated 6.1 years ago by
Michael Love
41k • written 6.1 years ago by
Moose123
• 0
0
votes
6
replies
1.5k
views
weird behaviour DESeq2 1.18.1
deseq2
outliers
version
updated 6.1 years ago by
Michael Love
41k • written 6.1 years ago by
aec
▴ 90
0
votes
4
replies
1.3k
views
significant genes with DESeq2 plenty of outliers and zero counts
zero counts
deseq2
odd results
outliers
updated 6.1 years ago by
Michael Love
41k • written 6.1 years ago by
aec
▴ 90
0
votes
1
reply
1.2k
views
Handling outliers in Deseq2
outliers
deseq2
logfoldchange
6.2 years ago
lirongrossmann
▴ 80
0
votes
10
replies
17k
views
Differential expression due to extreme outliers in DESeq2
deseq2
outliers
6.3 years ago
paul.alto
▴ 50
1
vote
3
replies
5.1k
views
DESeq2: How to manually perform filtering and outlier detection?
deseq2
filtering
outliers
count outliers
updated 6.6 years ago by
Wolfgang Huber
★ 13k • written 6.6 years ago by
heikki.sarin
▴ 10
0
votes
4
replies
2.3k
views
DESeq2, outlier correction, Combat, NMF
deseq2
combat
outliers
NMF
updated 6.8 years ago by
Michael Love
41k • written 6.8 years ago by
noname
• 0
1
vote
1
reply
1.3k
views
Outliers - to remove or to not remove that is the question
outliers
rna
microarray
updated 6.8 years ago by
chris86
▴ 420 • written 6.8 years ago by
bhgyu
▴ 30
1
vote
8
replies
3.0k
views
[DESeq2] Automatic outlier detection and replacement with continuous variables
deseq2
outliers
RNAseq
differential gene expression
7.0 years ago
cajawe
• 0
0
votes
9
replies
1.7k
views
DESeq2 influence of 2 samples
deseq2
outliers
differential gene expression
updated 7.2 years ago by
Michael Love
41k • written 7.2 years ago by
gregory.l.stone
▴ 10
0
votes
7
replies
3.5k
views
Deciding on cooks cutoff value DESeq2
deseq2
differential gene expression
outliers
bioconductor
updated 7.2 years ago by
Michael Love
41k • written 7.2 years ago by
gregory.l.stone
▴ 10
0
votes
3
replies
1.0k
views
DESeq outlier detection for unbalanced groups
deseq2
deseq
outliers
updated 7.7 years ago by
Michael Love
41k • written 7.7 years ago by
akaever
▴ 30
3
votes
3
replies
1.6k
views
How to define an outlier array from PCA?
microarray
PCA
outliers
sample outliers
limma
updated 8.2 years ago by
Aaron Lun
★ 28k • written 8.2 years ago by
serpalma.v
▴ 60
0
votes
0
replies
2.2k
views
Modeling count data that is zero inflated with negative binomial hurdle regression
pscl
outliers
updated 9.0 years ago by
Sean Davis
21k • written 9.0 years ago by
mrk.carty
▴ 30
8
votes
17
replies
14k
views
WGCNA for RNA-Seq Sample Set, Outliers, and Spearman correlation
WGCNA
Sample Size
Outliers
updated 8.6 years ago by
mh.manoj
• 0 • written 9.1 years ago by
brohawndg
▴ 150
25 results • Page
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Answer: New genes that did not exist in dds object suddenly showed up after degPatterns
by
Michael Love
41k
May be documented by the software you are using? https://github.com/lpantano/DEGreport
Answer: Doing comparison of RNA-seq data using Deseq2
by
Michael Love
41k
Take a look at our workflow, this starts from a beginner's level. You could export from Excel using CSV or TSV, then read into R. htt…
Answer: WGCNA: analysis of complex trait associations with regressions
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This support site is meant to help people with questions about Bioconductor packages (WGCNA is not a Bioconductor package). You might try o…
Comment: miRTarRnaseq library
by
mercedeh.movassagh
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Yes that is correct
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
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It is the minimum group size rather than the total number of samples that is relevant. `min.prop` is more a biological parameter rather th…
Votes
transcript name mapping between human and mouse
transcript name mapping between human and mouse
A: Error object and replacement value dimnames differ, when changing column names o
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
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