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Showing :
BatchEffect
•
reset
0
votes
0
replies
28
views
Batch effect correction: methylome data
sesame
BatchEffect
MethylationArray
16 hours ago
Seungmin
• 0
2
votes
9
replies
407
views
Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2
RUVSeq
RUVseq
BatchEffect
DES
updated 17 days ago by
James W. MacDonald
65k • written 17 days ago by
Alexandre
• 0
0
votes
2
replies
224
views
RNAseq:Technical replicates from different batches
technicalReplicates
BatchEffect
limma
RNASeq
23 days ago • updated 20 days ago
catv
• 0
2
votes
5
replies
1.2k
views
DESeq2 remove batch effect
BatchEffect
RNASeqData
WGCNA
DESeq2
updated 25 days ago by
Ashley
• 0 • written 11 months ago by
zxc741xb
• 0
0
votes
4
replies
613
views
How to correct for known and surrogate variables in DESeq2?
DESeq2
BatchEffect
sva
limma
updated 26 days ago by
Michael Love
42k • written 6 months ago by
Crystal571
• 0
0
votes
8
replies
435
views
DESeq and SVA for batch effect
DESeq2
BatchEffect
sva
9 weeks ago
michelafrancesconi8
• 0
1
vote
3
replies
376
views
DESEQ2 Batch Effect
DESeq2
BatchEffect
RNASeq
updated 9 weeks ago by
swbarnes2
★ 1.4k • written 10 weeks ago by
sap275
▴ 10
0
votes
0
replies
161
views
Can I combine collinear variables into a single value
BatchEffect
limma
10 weeks ago
Harrsha
• 0
2
votes
1
reply
271
views
Limma Question
DESeq2
BatchEffect
limma
RNASeq
updated 10 weeks ago by
Michael Love
42k • written 11 weeks ago by
sap275
▴ 10
0
votes
1
reply
330
views
When should I correct for batch effects
BatchEffect
SingleCellExperiment
updated 3 months ago by
James W. MacDonald
65k • written 3 months ago by
NeuroDaniel
• 0
0
votes
5
replies
591
views
Can SVs identified from sva be used for removeBatchEffect() in DESeq2
sva
DESeq2
BatchEffect
limma
updated 4 months ago by
ATpoint
★ 4.1k • written 4 months ago by
Xiao
• 0
2
votes
4
replies
662
views
Correct the batch effect in methylation analysis in R
BatchEffect
limma
methylationArrayAnalysis
updated 5 months ago by
Gordon Smyth
50k • written 5 months ago by
kyj2226
• 0
1
vote
4
replies
647
views
controling for batch effect while preserving variation within repeated measures that unevenly distributed across batches
miRNA
BatchEffect
RNASeq
limma
6 months ago
Wending
• 0
0
votes
1
reply
458
views
Batch effect adjust in model matrix
BatchEffect
edgeR
updated 7 months ago by
ATpoint
★ 4.1k • written 7 months ago by
Giuseppe
• 0
3
votes
5
replies
878
views
Getting batch corrected counts after RUVSeq
BatchEffect
RUVSeq
RNASeq
DESeq2
updated 8 months ago by
ATpoint
★ 4.1k • written 8 months ago by
Shashank
• 0
2
votes
4
replies
1.2k
views
RNAseq : identical sample-sample distances after using limma::removeBatchEffect
DESeq2
RNASeq
BatchEffect
limma
updated 8 months ago by
Michael Love
42k • written 2.9 years ago by
athiebaut
• 0
0
votes
1
reply
627
views
How to identify the batch informations from the sample ID?
TCGAbiolinks
BatchQC
BatchEffect
updated 8 months ago by
wrab425
• 0 • written 14 months ago by
snijesh
▴ 20
2
votes
5
replies
1.3k
views
removing the batch effect for vst counts and defining the batches in removeBatchEffect function
DESeq2
BatchEffect
limma
updated 9 months ago by
Gordon Smyth
50k • written 9 months ago by
Sara
• 0
2
votes
3
replies
1.1k
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 9 months ago by
James W. MacDonald
65k • written 9 months ago by
D-Bug
▴ 10
3
votes
4
replies
885
views
lfcShrink() and batch effects in DESeq2
BatchEffect
lfcshrink
RNA-seq
DESeq2
9 months ago
Eva
▴ 10
0
votes
2
replies
632
views
smallRNA-seq analysis batch correction in limma
BatchEffect
limma
9 months ago
Eleonora
• 0
1
vote
1
reply
464
views
Best way to handle batch effects from difference Mice?
RNASeqData
BatchEffect
edgeR
limma
updated 10 months ago by
Gordon Smyth
50k • written 10 months ago by
Sara
• 0
2
votes
3
replies
1.2k
views
PCA for QC should include subset of top variable genes or full set of genes in RNAseq data?
BatchQC
RNASeqData
sva
BatchEffect
updated 10 months ago by
ATpoint
★ 4.1k • written 10 months ago by
amnahsiddiqa
▴ 10
0
votes
0
replies
394
views
How to go for Batch correction in RNA-seq expeiment conducted based on imbalanced Experimental design ?
RNASeqData
BatchEffect
sva
10 months ago
amnahsiddiqa
▴ 10
1
vote
1
reply
503
views
WGCNA Cluster batch effect
BatchEffect
TCGA
WGCNA
updated 10 months ago by
ATpoint
★ 4.1k • written 10 months ago by
khaserdene99
• 0
1
vote
2
replies
987
views
Batch effect between biological replicates
BatchEffect
DESeq2
12 months ago
gtechbio
▴ 10
0
votes
4
replies
914
views
Combine RNA-seq
BatchEffect
R
rnaseq
updated 12 months ago by
swbarnes2
★ 1.4k • written 12 months ago by
Young Tae
• 0
2
votes
4
replies
1.5k
views
How to get TPM / FPKM after batch correction with DESeq2?
DESeq2
BatchEffect
tpm
fpkm
13 months ago
vk
• 0
2
votes
2
replies
896
views
Error in checkFullRank(modelMatrix)
DESeq2
BatchEffect
DifferentialExpression
updated 13 months ago by
ATpoint
★ 4.1k • written 13 months ago by
AZ
▴ 30
2
votes
3
replies
912
views
Batch correction and Deseq2
DESeq2
WGCNA
Normalization
NormalyzerDE
BatchEffect
updated 13 months ago by
ATpoint
★ 4.1k • written 14 months ago by
suphamon.j
▴ 20
3
votes
2
replies
755
views
Batch question Bulk RNA-Seq
BatchEffect
RNASeq
14 months ago
chf
• 0
2
votes
1
reply
1.5k
views
DESeq2 design after combatseq batch correction
DESeq2
BatchEffect
updated 14 months ago by
ATpoint
★ 4.1k • written 14 months ago by
Tyroone
• 0
0
votes
1
reply
487
views
Analysis with Batch correction
DESeq2
BatchEffect
updated 14 months ago by
Michael Love
42k • written 15 months ago by
giulia.lopatriello
• 0
1
vote
1
reply
761
views
Batch effect: Is it correct to put ~0 preparing the model.matrix to remove batch effect?
edgeR
model.matrix
BatchEffect
updated 15 months ago by
James W. MacDonald
65k • written 15 months ago by
greta
• 0
5
votes
2
replies
780
views
Sva and batch effect
limma
BatchEffect
sva
updated 15 months ago by
Gordon Smyth
50k • written 15 months ago by
Lenny186
• 0
1
vote
1
reply
1.7k
views
batch effect correction before DESeq2 analysis
DESeq2
BatchEffect
updated 15 months ago by
ATpoint
★ 4.1k • written 15 months ago by
luca.s
▴ 50
0
votes
0
replies
743
views
Trying to use a NanoString expression set with batch effects to do GSVA
GSVA
Normalization
BatchEffect
GSVAdata
NanoString
16 months ago
Zhijie
• 0
1
vote
0
replies
682
views
Use scran's normalization by deconvolution for each individual sample or over all samples
scran
Normalization
scRNA
BatchEffect
16 months ago
r_grau
▴ 10
1
vote
2
replies
901
views
Design formula with batch effects DESeq2 "Not full rank matrix" error.
DESeq2
BatchEffect
RNASeq
updated 18 months ago by
swbarnes2
★ 1.4k • written 18 months ago by
Flavio
• 0
3
votes
10
replies
1.9k
views
Fold Change calculation when Batch Effect is present in RNA-seq data (DEseq2)
DESeq2
BatchEffect
fold
19 months ago • updated 18 months ago
eve.olszanowski
• 0
1
vote
2
replies
804
views
Modelling batch effect in DESeq2 - how to interpret the results?
DESeq2
BatchEffect
19 months ago
annamariabugaj
▴ 10
0
votes
1
reply
983
views
Batch effects in DESeq2: determination and model building
BatchEffect
batch
RNASeqR
formula
DESeq2
updated 20 months ago by
Michael Love
42k • written 21 months ago by
estafana.t98
• 0
0
votes
1
reply
882
views
Building model matrix to correct for batch effect with biological and technical replicates: Problem with linear correlations
MassSpectrometryData
BatchEffect
r
limma
updated 21 months ago by
Gordon Smyth
50k • written 21 months ago by
mfaleevs
• 0
6
votes
7
replies
1.9k
views
Batch effect with one sample being in two batches
BatchEffect
DESeq2
23 months ago
lmrogers34
▴ 10
1
vote
1
reply
710
views
RNA-Seq normalization and batch effect removal
RNASeq
BatchEffect
DESeq2
updated 23 months ago by
Michael Love
42k • written 23 months ago by
Alexandre
• 0
2
votes
1
reply
1.3k
views
removeBatchEffect: Coefficients not estimable when using "batch matrix" for `covariates` argument.
limma
BatchEffect
updated 23 months ago by
Gordon Smyth
50k • written 23 months ago by
nhaus
▴ 30
0
votes
1
reply
947
views
Differential methilation analysis batch effect removal
BatchEffect
combat
sva
edgeR
RRBSdata
updated 2.1 years ago by
Gordon Smyth
50k • written 2.1 years ago by
Mageiros
• 0
1
vote
1
reply
1.1k
views
How to determine if limma can adjust for batch effect
BatchEffect
limma
sva
DifferentialExpression
updated 2.2 years ago by
ATpoint
★ 4.1k • written 2.2 years ago by
nhaus
▴ 30
0
votes
0
replies
508
views
Is it possible to do batch correction on Ht-Seq raw counts instead of using normalized counts? What's the difference?
Normalisedcounts
Rawcounts
Ht-SeqRNAData
BatchEffect
2.2 years ago
Ety
• 0
1
vote
7
replies
1.3k
views
Comparison DESeq results using different model
Batch
BatchEffect
DESeq2
updated 2.2 years ago by
James W. MacDonald
65k • written 2.2 years ago by
dequattro.concetta
▴ 10
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