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sva
•
reset
0
votes
3
replies
320
views
Meta-analysis on RNA-seq data sets
meta-analysis
sva
Combat_Seq
RNAseq
29 days ago • updated 28 days ago
Travis
• 0
4
votes
5
replies
11k
views
[sva] Error in density.default(x, adjust = adj) : 'x' contains missing values
sva
updated 9 weeks ago by
ndphuc1605
• 0 • written 7.0 years ago by
anton.kratz
▴ 60
0
votes
4
replies
798
views
Generating surrogate variables across multiple variables of interest
sva
3 months ago
Robert
• 0
0
votes
3
replies
635
views
A ComBat-seq issue: the covariates are confounded
ComBat-seq
sva
updated 6 months ago by
W. Evan Johnson
▴ 860 • written 6 months ago by
schlumbohm
• 0
3
votes
6
replies
760
views
Surrogate variable analysis for paired RNA seq experiment
RUVSeq
sva
6 months ago
nhaus
▴ 70
0
votes
2
replies
410
views
pca with VST of DESeq2 give 100% variance in PC1
DESeq2
sva
6 months ago
michelafrancesconi8
• 0
0
votes
4
replies
772
views
Adjust RNA-seq counts (more than one batch variable) for plotting differentially expressed genes
ComBat
sva
edgeR
6 months ago
Lucy
▴ 60
0
votes
8
replies
793
views
DESeq and SVA for batch effect
DESeq2
BatchEffect
sva
7 months ago
michelafrancesconi8
• 0
0
votes
3
replies
536
views
Would I treat surrogate variables as batches?
DESeq2
sva
updated 7 months ago by
James W. MacDonald
67k • written 7 months ago by
MEME
▴ 10
0
votes
5
replies
1.1k
views
Can SVs identified from sva be used for removeBatchEffect() in DESeq2
sva
DESeq2
BatchEffect
limma
updated 9 months ago by
ATpoint
★ 4.5k • written 9 months ago by
Xiao
• 0
0
votes
1
reply
634
views
DESeq2 interaction term + sva
sva
DESeq2
updated 9 months ago by
Michael Love
42k • written 10 months ago by
marinaw
▴ 20
0
votes
2
replies
548
views
combat output NaN
sva
11 months ago
maxixian1990
• 0
0
votes
4
replies
898
views
How to correct for known and surrogate variables in DESeq2?
DESeq2
BatchEffect
sva
limma
updated 6 months ago by
Michael Love
42k • written 12 months ago by
Crystal571
• 0
5
votes
2
replies
1.5k
views
ComBat_seq function in sva package does not return a matrix
sva
ComBat
ComBat-seq
Bioconductor
ComBat_seq
13 months ago
Federico
▴ 10
5
votes
9
replies
1.8k
views
Batch correction and repeated measures
RUVSeq
sva
limma
updated 6 months ago by
Gordon Smyth
51k • written 13 months ago by
Jonathan
▴ 10
0
votes
1
reply
723
views
SVA for MatrixeQTL - which "variable of interest"?
matrixeqtl
sva
updated 14 months ago by
James W. MacDonald
67k • written 14 months ago by
Shila
• 0
2
votes
3
replies
1.8k
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 14 months ago by
James W. MacDonald
67k • written 14 months ago by
D-Bug
▴ 10
0
votes
2
replies
843
views
Fluidigm Data Batch Correction
sva
limma
updated 15 months ago by
Gordon Smyth
51k • written 15 months ago by
Khushbu
• 0
3
votes
3
replies
1.5k
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
16 months ago
amnahsiddiqa
▴ 10
2
votes
3
replies
1.8k
views
PCA for QC should include subset of top variable genes or full set of genes in RNAseq data?
BatchQC
RNASeqData
sva
BatchEffect
updated 16 months ago by
ATpoint
★ 4.5k • written 16 months ago by
amnahsiddiqa
▴ 10
0
votes
0
replies
540
views
How to go for Batch correction in RNA-seq expeiment conducted based on imbalanced Experimental design ?
RNASeqData
BatchEffect
sva
16 months ago
amnahsiddiqa
▴ 10
0
votes
1
reply
751
views
Normalization of RNA seq data before DESeq2 and PCA in case of strong batch effects
DESeq2
Normalization
sva
updated 19 months ago by
ATpoint
★ 4.5k • written 19 months ago by
marslena
• 0
2
votes
2
replies
1.1k
views
Updating DESeq2 object's design with sva output
DESeq2
design
sva
20 months ago
Hatchet
• 0
5
votes
2
replies
1.0k
views
Sva and batch effect
limma
BatchEffect
sva
updated 21 months ago by
Gordon Smyth
51k • written 21 months ago by
Lenny186
• 0
0
votes
2
replies
1.0k
views
DESeq2 LFC changes sign after adjusting for surrogates
sva
DESeq2
2.2 years ago
Marie
• 0
2
votes
9
replies
2.0k
views
Remove unwanted variation/confounder due to library size with sva
sva
updated 2.2 years ago by
James W. MacDonald
67k • written 2.3 years ago by
Jasmin
• 0
1
vote
0
replies
800
views
Why does surrogate variable confound with variable given in mod?
sva
2.3 years ago
shdam
▴ 10
1
vote
3
replies
1.6k
views
Error in shrinkage for DESeq2
sva
DESeq2
2.4 years ago
Kent
• 0
1
vote
1
reply
890
views
paired analysis : return data matrix with indvidual/subject effects eliminated.
RUVSeq
sva
DESeq2
updated 2.4 years ago by
James W. MacDonald
67k • written 2.4 years ago by
ramonfallon
▴ 20
1
vote
2
replies
2.0k
views
Is it necessary to standardize Combat in R?
RNA
Combat
sva
R
2.4 years ago
takemoto
• 0
0
votes
1
reply
1.2k
views
Differential methilation analysis batch effect removal
BatchEffect
combat
sva
edgeR
RRBSdata
updated 2.5 years ago by
Gordon Smyth
51k • written 2.5 years ago by
Mageiros
• 0
1
vote
1
reply
1.4k
views
How to determine if limma can adjust for batch effect
BatchEffect
limma
sva
DifferentialExpression
updated 2.7 years ago by
ATpoint
★ 4.5k • written 2.7 years ago by
nhaus
▴ 70
1
vote
4
replies
2.0k
views
incorporating batch into DESeq2 design after batch correction with combatseq
DESeq2
sva
2.7 years ago
Clay
• 0
0
votes
0
replies
1.2k
views
SVA method for estimating surrogate variables of RNA Seq
RNASeq
sva
svaseq
updated 2.8 years ago by
James W. MacDonald
67k • written 2.8 years ago by
Bex
• 0
0
votes
5
replies
4.4k
views
How to remove batch effect from RNA-seq without count data?
RUVSeq
FPKM
removeBatchEffect
RNA-seq
sva
updated 2.8 years ago by
ATpoint
★ 4.5k • written 3.6 years ago by
Xiaojie Cheng
• 0
0
votes
0
replies
932
views
SVAseq for differential transcript usage and differential splicing analysis
limma
sva
Leafcutter
SVAseq
3.1 years ago
georgia.katsoula
▴ 40
1
vote
4
replies
6.9k
views
At least one covariate is confounded with batch! Please remove confounded covariates and rerun ComBat
ComBat
sva
3.1 years ago
NewBioInfo
▴ 10
1
vote
2
replies
1.6k
views
Confused about using ComBat_seq with voom and limma? Should run batch as a covariate and use uncorrected instead?
sva
limma
3.2 years ago
Ahdee
▴ 50
0
votes
1
reply
3.8k
views
SVA behaving weirdly, system is computationally singular , problem with method leek only
SVA
combat sva
leek
updated 3.4 years ago by
chase.mateusiak
• 0 • written 7.5 years ago by
amoltej
▴ 10
0
votes
1
reply
2.0k
views
Removing batch effect by sva or combat and subsequent correlation analysis by WGCNA
WGCNA
impute
sva
updated 3.4 years ago by
sebastian.lobentanzer
▴ 50 • written 3.4 years ago by
chiwut.wong
• 0
1
vote
4
replies
2.6k
views
ComBat Normalisation - data is integers and some floats, confused?!
combat
rnaseq
combatnormalisation
jeffleek
sva
updated 12 months ago by
Hamza
• 0 • written 3.6 years ago by
zeegzaag
• 0
0
votes
1
reply
1.6k
views
How to set mod0 in sva analysis
sva
updated 3.7 years ago by
Robert Castelo
★ 3.4k • written 3.7 years ago by
hank9cao
• 0
2
votes
2
replies
1.2k
views
Preprocessing Issue
sva
RNASeq
Preprocessing
Normalization
BatchEffect
updated 3.7 years ago by
ATpoint
★ 4.5k • written 3.7 years ago by
MOHAMMAD
• 0
0
votes
0
replies
1.1k
views
Surrogate variable, celltype composition correction and overfitting in DNA methylation data
sva
limma
methylation
MethylationArray
3.8 years ago
epibio
▴ 10
1
vote
8
replies
1.7k
views
Error in running Combat function
sva
ComBat
updated 3.8 years ago by
Kevin Blighe
★ 4.0k • written 3.8 years ago by
Reza
▴ 10
0
votes
5
replies
1.3k
views
Variable of interest in combat correction
sva
combat
updated 4.0 years ago by
James W. MacDonald
67k • written 4.0 years ago by
ch_el
▴ 10
0
votes
3
replies
1.3k
views
Extracting a subset of samples following SVA
Combat
SVA
Limma
updated 4.1 years ago by
Kevin Blighe
★ 4.0k • written 4.1 years ago by
jonellevillar
• 0
0
votes
10
replies
1.4k
views
Running SVA changes format of time variable in model
sva
proxitct
hms
updated 4.1 years ago by
James W. MacDonald
67k • written 4.1 years ago by
jonellevillar
• 0
7
votes
6
replies
2.1k
views
sva ComBat implementation for multiple sources of batch effects
sva
combat
batch-adjustment
updated 4.5 years ago by
W. Evan Johnson
▴ 860 • written 4.5 years ago by
Zach Roe
▴ 10
0
votes
1
reply
926
views
SVA for visualisation purposes
sva
svaseq
surrogate variable analysis
updated 4.5 years ago by
James W. MacDonald
67k • written 4.5 years ago by
Mozart
▴ 30
50 results • Page
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Recent ...
Replies
Answer: Analysis of 2*4 factorial design
by
Gordon Smyth
51k
This is covered by Section 9.5 of the limma User's Guide. The analysis with a single-factor is much better. Your definition of A2 vs A1 …
Comment: Zero intra-block correlation in RRBS analysis using voomLmFit with block
by
Gordon Smyth
51k
It might be ok to estimate the intrablock correlation from the M-values. But then, if you do that, you may as well do the whole analysis in…
Answer: limma technical repeat correction
by
Gordon Smyth
51k
The technical samples should be averaged. Then use duplicateCorrelation() with block=PatientID.
Comment: New to mass spec data analysis
by
abhisek001
• 0
Thanks for your kind responses.
Comment: Duplicate row.names when building SummarizedExperiment with make_se in DEP
by
Anni
• 0
I encountered the same problem. Problem seems to be "make_se()" function that does *not* use variable 'label' to bind colData to assay, but…
Votes
Differential expression analysis starting from TPM data
Answer: How to identify top most variable genes from log2 normalized data?
Answer: How to identify top most variable genes from log2 normalized data?
Answer: clusterProfiler enrichGO on only T-cell related GO terms
Answer: clusterProfiler enrichGO on only T-cell related GO terms
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