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Showing :
batcheffect
•
reset
6
votes
7
replies
1.8k
views
Batch effect with one sample being in two batches
BatchEffect
DESeq2
22 months ago
lmrogers34
▴ 10
6
votes
4
replies
11k
views
How to use combat in order to remove batch effects?
BatchEffect
DESeq2
RNASeqData
updated 2.3 years ago by
BioNovice247
• 0 • written 3.1 years ago by
Emma
▴ 10
6
votes
6
replies
1.4k
views
Batch effect from to sequencing data at differents depths
Sequencing
sequencingDeepth
BatchEffect
DESeq2
2.5 years ago
ary.lech
▴ 10
6
votes
4
replies
4.0k
views
Merge different datasets and perform differential expression analysis in limma
insilicomerging
batcheffect
limma
differential gene expression
bioconductor
updated 8.8 years ago by
Aaron Lun
★ 28k • written 8.8 years ago by
svlachavas
▴ 830
5
votes
2
replies
761
views
Sva and batch effect
limma
BatchEffect
sva
updated 15 months ago by
Gordon Smyth
50k • written 15 months ago by
Lenny186
• 0
4
votes
10
replies
2.0k
views
Subject: Strange glitch in Voom curve resulting from batch effects
limma
voom
batcheffect
covariate
updated 7.0 years ago by
Gordon Smyth
50k • written 7.0 years ago by
raf4
▴ 20
3
votes
10
replies
1.9k
views
Fold Change calculation when Batch Effect is present in RNA-seq data (DEseq2)
DESeq2
BatchEffect
fold
18 months ago
eve.olszanowski
• 0
3
votes
6
replies
3.0k
views
RNAseq multifactor experiment limma design with patient and batch effects
limma
rnaseq
batcheffect
updated 8.9 years ago by
robert.maughan
• 0 • written 9.5 years ago by
cfreije
▴ 10
3
votes
6
replies
2.2k
views
is it necessary to check batch effect in this case? and how to?
svaseq
combat sva
RANseq
batcheffect
removebatcheffect
updated 7.5 years ago by
Jakub
▴ 50 • written 7.5 years ago by
amoltej
▴ 10
3
votes
2
replies
726
views
Batch question Bulk RNA-Seq
BatchEffect
RNASeq
13 months ago
chf
• 0
3
votes
5
replies
826
views
Getting batch corrected counts after RUVSeq
BatchEffect
RUVSeq
RNASeq
DESeq2
updated 7 months ago by
ATpoint
★ 4.0k • written 7 months ago by
Shashank
• 0
3
votes
4
replies
854
views
lfcShrink() and batch effects in DESeq2
BatchEffect
lfcshrink
RNA-seq
DESeq2
8 months ago
Eva
▴ 10
2
votes
4
replies
1.4k
views
How to get TPM / FPKM after batch correction with DESeq2?
DESeq2
BatchEffect
tpm
fpkm
12 months ago
vk
• 0
2
votes
1
reply
1.6k
views
EdgeR: Accounting for batch effects in a pairwise analysis
paired
batcheffect
updated 9.2 years ago by
Gordon Smyth
50k • written 9.2 years ago by
cinderelliedoll
• 0
2
votes
3
replies
2.8k
views
Questions in limma about multifactorial design and possible batch effect correction
limma
batcheffect
batcheffectcorrection
multiple factor design
updated 9.0 years ago by
James W. MacDonald
65k • written 9.0 years ago by
svlachavas
▴ 830
2
votes
4
replies
4.9k
views
edgeR and batch effect correction for differential analysis
edger
limma
r
rnaseq
batcheffect
updated 5.0 years ago by
James W. MacDonald
65k • written 5.0 years ago by
m93
• 0
2
votes
2
replies
1.0k
views
Addressing the batch effect in multifactor experiment
edgeR
BatchEffect
RNASeq
updated 3.4 years ago by
SamGG
▴ 350 • written 3.4 years ago by
anikng
▴ 10
2
votes
2
replies
975
views
Preprocessing Issue
sva
RNASeq
Preprocessing
Normalization
BatchEffect
updated 3.2 years ago by
ATpoint
★ 4.0k • written 3.2 years ago by
MOHAMMAD
• 0
2
votes
4
replies
1.2k
views
RNAseq : identical sample-sample distances after using limma::removeBatchEffect
DESeq2
RNASeq
BatchEffect
limma
updated 7 months ago by
Michael Love
41k • written 2.9 years ago by
athiebaut
• 0
2
votes
1
reply
1.4k
views
DESeq2 design after combatseq batch correction
DESeq2
BatchEffect
updated 14 months ago by
ATpoint
★ 4.0k • written 14 months ago by
Tyroone
• 0
2
votes
4
replies
615
views
Correct the batch effect in methylation analysis in R
BatchEffect
limma
methylationArrayAnalysis
updated 4 months ago by
Gordon Smyth
50k • written 4 months ago by
kyj2226
• 0
2
votes
3
replies
1.1k
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
★ 4.0k • written 10 months ago by
amnahsiddiqa
▴ 10
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
2
votes
5
replies
1.1k
views
DESeq2 remove batch effect
BatchEffect
RNASeqData
WGCNA
DESeq2
updated 9 days ago by
Ashley
• 0 • written 10 months ago by
zxc741xb
• 0
2
votes
3
replies
879
views
Batch correction and Deseq2
DESeq2
WGCNA
Normalization
NormalyzerDE
BatchEffect
updated 13 months ago by
ATpoint
★ 4.0k • written 13 months ago by
suphamon.j
▴ 20
2
votes
2
replies
958
views
Does MNN removes same average batch vector from all cells or each cell has it's own correction vector?
fastmnn
batchelor
BatchEffect
2.6 years ago
p.joshi
▴ 40
2
votes
2
replies
857
views
Error in checkFullRank(modelMatrix)
DESeq2
BatchEffect
DifferentialExpression
updated 12 months ago by
ATpoint
★ 4.0k • written 12 months ago by
AZ
▴ 30
2
votes
1
reply
247
views
Limma Question
DESeq2
BatchEffect
limma
RNASeq
updated 8 weeks ago by
Michael Love
41k • written 8 weeks ago by
sap275
▴ 10
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 8 months ago by
James W. MacDonald
65k • written 8 months ago by
D-Bug
▴ 10
2
votes
9
replies
274
views
Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2
RUVSeq
RUVseq
BatchEffect
DES
updated 1 day ago by
James W. MacDonald
65k • written 1 day ago by
Alexandre
• 0
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 8 months ago by
Gordon Smyth
50k • written 8 months ago by
Sara
• 0
1
vote
1
reply
743
views
Batch effect: Is it correct to put ~0 preparing the model.matrix to remove batch effect?
edgeR
model.matrix
BatchEffect
updated 14 months ago by
James W. MacDonald
65k • written 14 months ago by
greta
• 0
1
vote
5
replies
1.9k
views
Appropriate merge of batches of the same array to create a final total ExpressionSet
frma
bioconductor
batcheffect
Primeview
insilicomerging
updated 9.0 years ago by
Matthew McCall
▴ 830 • written 9.0 years ago by
svlachavas
▴ 830
1
vote
2
replies
962
views
Batch effect between biological replicates
BatchEffect
DESeq2
11 months ago
gtechbio
▴ 10
1
vote
1
reply
489
views
WGCNA Cluster batch effect
BatchEffect
TCGA
WGCNA
updated 10 months ago by
ATpoint
★ 4.0k • written 10 months ago by
khaserdene99
• 0
1
vote
15
replies
2.5k
views
between and within subjects design with batch correction
RNASeqData
BatchEffect
paired
DESeq2
3.0 years ago
demisa
• 0
1
vote
1
reply
997
views
Combining treatment and control batches for analysis
scRNAseq
scRNA
batchelor
BatchEffect
updated 3.4 years ago by
Aaron Lun
★ 28k • written 3.5 years ago by
Adrien
• 0
1
vote
5
replies
2.6k
views
Deseq2 - removing batch effect
BatchEffect
DESeq2
updated 3.0 years ago by
Kevin Blighe
★ 3.9k • written 3.0 years ago by
vinisha
• 0
1
vote
1
reply
1.3k
views
DESeq2 batch effects
BatchEffect
DESeq2
RNASeq
updated 3.5 years ago by
Michael Love
41k • written 3.5 years ago by
igor
▴ 40
1
vote
1
reply
697
views
RNA-Seq normalization and batch effect removal
RNASeq
BatchEffect
DESeq2
updated 22 months ago by
Michael Love
41k • written 22 months ago by
Alexandre
• 0
1
vote
0
replies
658
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
1
reply
448
views
Best way to handle batch effects from difference Mice?
RNASeqData
BatchEffect
edgeR
limma
updated 9 months ago by
Gordon Smyth
50k • written 9 months ago by
Sara
• 0
1
vote
2
replies
878
views
Is 100K genes too many to run ComBat_seq on?
RNASeqRData
combat_Seq
BatchEffect
2.6 years ago • updated 2.3 years ago
zeegzaag
• 0
1
vote
2
replies
880
views
Design formula with batch effects DESeq2 "Not full rank matrix" error.
DESeq2
BatchEffect
RNASeq
updated 18 months ago by
swbarnes2
★ 1.3k • written 18 months ago by
Flavio
• 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
★ 4.0k • written 2.2 years ago by
nhaus
▴ 30
1
vote
4
replies
613
views
controling for batch effect while preserving variation within repeated measures that unevenly distributed across batches
miRNA
BatchEffect
RNASeq
limma
5 months ago
Wending
• 0
1
vote
6
replies
1.6k
views
edgeR removing batch effect before using expression data for clustering
edger
r
batcheffect
clustering
removeBatchEffect
updated 5.0 years ago by
James W. MacDonald
65k • written 5.0 years ago by
Biologist
▴ 110
1
vote
3
replies
944
views
Limma: Differential expression with two batch effects , location and batch.
duplicatecorrelation
BatchEffect
limma
corfit
updated 3.4 years ago by
Gordon Smyth
50k • written 3.4 years ago by
Katherine
• 0
1
vote
5
replies
1.1k
views
Group Specific Condition Query
deseq2
deseq
batcheffect
updated 5.7 years ago by
Michael Love
41k • written 5.7 years ago by
bdy8
▴ 10
1
vote
1
reply
1.6k
views
batch effect correction before DESeq2 analysis
DESeq2
BatchEffect
updated 15 months ago by
ATpoint
★ 4.0k • written 15 months ago by
luca.s
▴ 50
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