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sva
•
reset
0
votes
3
replies
247
views
DESeq2 - how many surrogate variables from svaseq, use of lfcshrink
sva
lfcshrink
DESeq2
written 27 days ago by
ja569116
• 0
0
votes
0
replies
348
views
Combining COMBAT-seq result (raw count) with other raw count
rnaseq
combat-seq
sva
combat
bulk-rnaseq
8 months ago
dudwnsrla1
• 0
0
votes
1
reply
782
views
Combat-seq usage
sva
8 months ago • updated 7 months ago
bbao
▴ 10
0
votes
0
replies
420
views
Batch correction for microarray
BatchEffect
sva
MicroarrayData
9 months ago
Shaimaa Gamal
• 0
1
vote
1
reply
1.1k
views
ComBat with repeated measures
ComBat
sva
updated 9 months ago by
ATpoint
★ 5.0k • written 9 months ago by
s20
• 0
3
votes
5
replies
1.7k
views
Overcoming confounding in batch effect correction
sva
BiologicalQuestion
11 months ago
bbao
▴ 10
0
votes
2
replies
999
views
sva: get a sv for RIN scores
limma
sva
variancePartition
voom
RNASeq
updated 13 months ago by
Gordon Smyth
53k • written 13 months ago by
Lina
▴ 10
0
votes
3
replies
1.3k
views
Meta-analysis on RNA-seq data sets
meta-analysis
sva
Combat_Seq
RNAseq
15 months ago
Travis
• 0
4
votes
5
replies
13k
views
[sva] Error in density.default(x, adjust = adj) : 'x' contains missing values
sva
updated 17 months ago by
ndphuc1605
• 0 • written 8.3 years ago by
anton.kratz
▴ 60
0
votes
4
replies
1.6k
views
Generating surrogate variables across multiple variables of interest
sva
18 months ago • updated 17 months ago
Robert
• 0
0
votes
3
replies
1.8k
views
A ComBat-seq issue: the covariates are confounded
ComBat-seq
sva
updated 21 months ago by
W. Evan Johnson
▴ 870 • written 21 months ago by
schlumbohm
• 0
3
votes
6
replies
1.7k
views
Surrogate variable analysis for paired RNA seq experiment
RUVSeq
sva
21 months ago
nhaus
▴ 70
0
votes
2
replies
780
views
pca with VST of DESeq2 give 100% variance in PC1
DESeq2
sva
21 months ago
michelafrancesconi8
• 0
0
votes
4
replies
1.6k
views
Adjust RNA-seq counts (more than one batch variable) for plotting differentially expressed genes
ComBat
sva
edgeR
21 months ago
Lucy
▴ 60
0
votes
8
replies
1.7k
views
DESeq and SVA for batch effect
DESeq2
BatchEffect
sva
22 months ago
michelafrancesconi8
• 0
0
votes
3
replies
988
views
Would I treat surrogate variables as batches?
DESeq2
sva
updated 22 months ago by
James W. MacDonald
68k • written 22 months ago by
MEME
▴ 10
0
votes
5
replies
2.1k
views
Can SVs identified from sva be used for removeBatchEffect() in DESeq2
sva
DESeq2
BatchEffect
limma
updated 2.0 years ago by
ATpoint
★ 5.0k • written 2.0 years ago by
Xiao
• 0
0
votes
1
reply
1.1k
views
DESeq2 interaction term + sva
sva
DESeq2
updated 2.0 years ago by
Michael Love
43k • written 2.1 years ago by
marinaw
▴ 20
0
votes
2
replies
962
views
combat output NaN
sva
2.2 years ago
maxixian1990
• 0
0
votes
4
replies
1.5k
views
How to correct for known and surrogate variables in DESeq2?
DESeq2
BatchEffect
sva
limma
updated 21 months ago by
Michael Love
43k • written 2.2 years ago by
Crystal571
• 0
5
votes
2
replies
3.0k
views
ComBat_seq function in sva package does not return a matrix
sva
ComBat
ComBat-seq
Bioconductor
ComBat_seq
2.3 years ago
Federico
▴ 10
5
votes
9
replies
2.9k
views
Batch correction and repeated measures
RUVSeq
sva
limma
updated 21 months ago by
Gordon Smyth
53k • written 2.3 years ago by
Jonathan
▴ 10
0
votes
1
reply
1.1k
views
SVA for MatrixeQTL - which "variable of interest"?
matrixeqtl
sva
updated 2.4 years ago by
James W. MacDonald
68k • written 2.4 years ago by
Shila
• 0
2
votes
3
replies
3.2k
views
bulk RNA-seq analysis using R : batch effect : One question concerning Combat-seq and one question concerning DESeq2 design = batch + condition
BatchEffect
sva
DESeq2
RNASeqData
limma
updated 2.4 years ago by
James W. MacDonald
68k • written 2.4 years ago by
D-Bug
▴ 10
0
votes
2
replies
1.2k
views
Fluidigm Data Batch Correction
sva
limma
updated 2.5 years ago by
Gordon Smyth
53k • written 2.5 years ago by
Khushbu
• 0
3
votes
3
replies
2.7k
views
how to remove batch effects of RNA seq data based on continuous variables(like surrogate variables from sva package) using combatseq or limma (remove…
combatseq
RNASeqData
sva
limma
2.5 years ago
amnahsiddiqa
▴ 10
2
votes
3
replies
2.7k
views
PCA for QC should include subset of top variable genes or full set of genes in RNAseq data?
BatchQC
RNASeqData
sva
BatchEffect
updated 2.5 years ago by
ATpoint
★ 5.0k • written 2.6 years ago by
amnahsiddiqa
▴ 10
0
votes
0
replies
909
views
How to go for Batch correction in RNA-seq expeiment conducted based on imbalanced Experimental design ?
RNASeqData
BatchEffect
sva
2.6 years ago
amnahsiddiqa
▴ 10
0
votes
1
reply
1.1k
views
Normalization of RNA seq data before DESeq2 and PCA in case of strong batch effects
DESeq2
Normalization
sva
updated 2.9 years ago by
ATpoint
★ 5.0k • written 2.9 years ago by
marslena
• 0
2
votes
2
replies
1.4k
views
Updating DESeq2 object's design with sva output
DESeq2
design
sva
2.9 years ago
Hatchet
• 0
5
votes
2
replies
1.4k
views
Sva and batch effect
limma
BatchEffect
sva
updated 3.0 years ago by
Gordon Smyth
53k • written 3.0 years ago by
Lenny186
• 0
0
votes
2
replies
1.4k
views
DESeq2 LFC changes sign after adjusting for surrogates
sva
DESeq2
3.4 years ago
Marie
• 0
2
votes
9
replies
2.6k
views
Remove unwanted variation/confounder due to library size with sva
sva
updated 3.5 years ago by
James W. MacDonald
68k • written 3.5 years ago by
Jasmin
• 0
1
vote
0
replies
1.1k
views
Why does surrogate variable confound with variable given in mod?
sva
3.5 years ago
shdam
▴ 10
1
vote
3
replies
2.1k
views
Error in shrinkage for DESeq2
sva
DESeq2
3.6 years ago
Kent
• 0
1
vote
1
reply
1.2k
views
paired analysis : return data matrix with indvidual/subject effects eliminated.
RUVSeq
sva
DESeq2
updated 3.6 years ago by
James W. MacDonald
68k • written 3.6 years ago by
ramonfallon
▴ 20
1
vote
2
replies
2.7k
views
Is it necessary to standardize Combat in R?
RNA
Combat
sva
R
3.7 years ago • updated 3.6 years ago
takemoto
• 0
0
votes
1
reply
2.0k
views
Differential methilation analysis batch effect removal
BatchEffect
combat
sva
edgeR
RRBSdata
updated 3.8 years ago by
Gordon Smyth
53k • written 3.8 years ago by
Mageiros
• 0
1
vote
1
reply
2.1k
views
How to determine if limma can adjust for batch effect
BatchEffect
limma
sva
DifferentialExpression
updated 3.9 years ago by
ATpoint
★ 5.0k • written 3.9 years ago by
nhaus
▴ 70
1
vote
4
replies
2.7k
views
incorporating batch into DESeq2 design after batch correction with combatseq
DESeq2
sva
3.9 years ago
Clay
• 0
0
votes
0
replies
1.6k
views
SVA method for estimating surrogate variables of RNA Seq
RNASeq
sva
svaseq
updated 4.0 years ago by
James W. MacDonald
68k • written 4.0 years ago by
Bex
• 0
0
votes
5
replies
6.2k
views
How to remove batch effect from RNA-seq without count data?
RUVSeq
FPKM
removeBatchEffect
RNA-seq
sva
updated 4.0 years ago by
ATpoint
★ 5.0k • written 4.8 years ago by
Xiaojie Cheng
• 0
0
votes
0
replies
1.3k
views
SVAseq for differential transcript usage and differential splicing analysis
limma
sva
Leafcutter
SVAseq
4.3 years ago
georgia.katsoula
▴ 40
1
vote
4
replies
8.8k
views
At least one covariate is confounded with batch! Please remove confounded covariates and rerun ComBat
ComBat
sva
4.3 years ago
NewBioInfo
▴ 10
1
vote
2
replies
2.2k
views
Confused about using ComBat_seq with voom and limma? Should run batch as a covariate and use uncorrected instead?
sva
limma
4.4 years ago
Ahdee
▴ 60
0
votes
1
reply
4.5k
views
SVA behaving weirdly, system is computationally singular , problem with method leek only
SVA
combat sva
leek
updated 4.6 years ago by
chase.mateusiak
• 0 • written 8.7 years ago by
amoltej
▴ 10
0
votes
1
reply
2.8k
views
Removing batch effect by sva or combat and subsequent correlation analysis by WGCNA
WGCNA
impute
sva
updated 4.7 years ago by
sebastian.lobentanzer
▴ 60 • written 4.7 years ago by
chiwut.wong
• 0
1
vote
4
replies
3.8k
views
ComBat Normalisation - data is integers and some floats, confused?!
combat
rnaseq
combatnormalisation
jeffleek
sva
updated 2.2 years ago by
Hamza
• 0 • written 4.9 years ago by
zeegzaag
• 0
0
votes
1
reply
2.1k
views
How to set mod0 in sva analysis
sva
updated 4.9 years ago by
Robert Castelo
★ 3.4k • written 4.9 years ago by
hank9cao
• 0
2
votes
2
replies
1.6k
views
Preprocessing Issue
sva
RNASeq
Preprocessing
Normalization
BatchEffect
updated 4.9 years ago by
ATpoint
★ 5.0k • written 4.9 years ago by
MOHAMMAD
• 0
241 results • Page
1 of 5
Recent ...
Replies
Answer: When to use edgeR or limma
by
Gordon Smyth
53k
The short answer is that we generally prefer edgeR for applications with lots of small counts and limma for complex designs with random eff…
Comment: limpa-blank normalization and Spectronaut's PTM stoichiometry
by
Gordon Smyth
53k
I updated the above answer today.
Answer: When to use edgeR or limma
by
James W. MacDonald
68k
I would use edgeR's quasi-likelihood model for any analysis with a smaller number of observations (like 3 vs 3 or similar), but if you have…
Answer: limpa-blank normalization and Spectronaut's PTM stoichiometry
by
Gordon Smyth
53k
The short answer is that limpa reads standard feature-level intensities from Spectronaut or other quantifications tools. limpa is designed …
Comment: Question about the filterByExpr function inputs in edgeR
by
mohammedtoufiq91
▴ 10
@gordonsmyth Noted, thank you very much.
Votes
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
A: deseq2 - paired samples in 2 sequencing types with very different library sizes
Comment: Question about the filterByExpr function inputs in edgeR
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