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Batcheffect
•
reset
0
votes
4
replies
220
views
Is there a way to do DEG analysis across two batches sharing one sample only?
DESeq2
DifferentialExpression
RNASeqData
BatchEffect
12 days ago
georgeyu703
• 0
2
votes
9
replies
806
views
Why did PCA plots look exactly the same after adjusting for batch covariate in DESeq2 design?
DESeq2
BatchEffect
26 days ago • updated 14 days ago
Quang NN
▴ 10
2
votes
4
replies
1.7k
views
Differential Expression Analysis with unbalanced batches without replication between conditions
edgeR
BatchEffect
updated 12 weeks ago by
Gordon Smyth
52k • written 12 weeks ago by
Thili
• 0
0
votes
2
replies
603
views
Integration of Single Cell Experiments with batchelor::fastMNN
fastMNN
SingleCellData
BatchEffect
batchelor
3 months ago
José
• 0
0
votes
6
replies
911
views
[DESeq2] Introduce a bias in DESeq2
DifferentialExpression
DESeq2
BatchEffect
updated 3 months ago by
Michael Love
43k • written 3 months ago by
CriticalPeriod
• 0
5
votes
4
replies
544
views
How to control batch effect if Group and batch are same?
limma
DESeq2
BatchEffect
updated 3 months ago by
ATpoint
★ 4.6k • written 4 months ago by
Bioinformagician
• 0
0
votes
5
replies
752
views
heatmap with batch effect
DESeq2
BatchEffect
4 months ago • updated 3 months ago
tothuhien
• 0
2
votes
2
replies
399
views
Batch adjustment for cohort based RNA seq data
RNASeqPower
removeBatchEffect
cpm
Batcheffect
4 months ago
sukeshinik5
▴ 20
0
votes
2
replies
441
views
ReactomeGSA adjustment for confounding variables
BiologicalQuestion
ReactomeGSA
BatchEffect
written 5 months ago by
Shaimaa Gamal
• 0
4
votes
7
replies
1.4k
views
What does evidence of batch effect in bulk rnaseq look like?
surrogatevariables
DESeq2
BatchEffect
bulkrna-seq
sva-seq
updated 6 months ago by
jessica.mcclintock
▴ 10 • written 7 months ago by
BioinfGuru
▴ 70
2
votes
2
replies
595
views
Control group between 2 batches have different expression in RNAseq data
BatchQC
BatchEffect
rnaseqGene
Normalization
updated 8 months ago by
jessica.mcclintock
▴ 10 • written 8 months ago by
Đình Vinh
• 0
2
votes
2
replies
694
views
How to remove batch effect to combine RNAseq data from 2 different experiments?
BatchQC
BatchEffect
RNASeq
updated 8 months ago by
jessica.mcclintock
▴ 10 • written 8 months ago by
ttt
• 0
0
votes
1
reply
415
views
ReactomeGSA for RNASeq
ReactomeGSA
BatchEffect
RNASeqData
updated 5 months ago by
jg
▴ 20 • written 8 months ago by
Shaimaa Gamal
• 0
0
votes
2
replies
1.2k
views
Batch effect correction: methylome data
sesame
BatchEffect
MethylationArray
updated 8 months ago by
zhouwanding
▴ 20 • written 8 months ago by
Seungmin
• 0
2
votes
9
replies
1.1k
views
Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2
RUVSeq
RUVseq
BatchEffect
DES
updated 9 months ago by
James W. MacDonald
67k • written 9 months ago by
Alexandre
• 0
0
votes
2
replies
671
views
RNAseq:Technical replicates from different batches
technicalReplicates
BatchEffect
limma
RNASeq
9 months ago
catv
• 0
0
votes
8
replies
949
views
DESeq and SVA for batch effect
DESeq2
BatchEffect
sva
11 months ago
michelafrancesconi8
• 0
1
vote
3
replies
760
views
DESEQ2 Batch Effect
DESeq2
BatchEffect
RNASeq
updated 11 months ago by
swbarnes2
★ 1.4k • written 11 months ago by
sap275
▴ 10
0
votes
0
replies
408
views
Can I combine collinear variables into a single value
BatchEffect
limma
11 months ago
Harrsha
• 0
2
votes
1
reply
536
views
Limma Question
DESeq2
BatchEffect
limma
RNASeq
updated 11 months ago by
Michael Love
43k • written 11 months ago by
sap275
▴ 10
4
votes
1
reply
1.2k
views
When should I correct for batch effects
BatchEffect
SingleCellExperiment
updated 12 months ago by
James W. MacDonald
67k • written 12 months ago by
NeuroDaniel
▴ 20
0
votes
5
replies
1.4k
views
Can SVs identified from sva be used for removeBatchEffect() in DESeq2
sva
DESeq2
BatchEffect
limma
updated 13 months ago by
ATpoint
★ 4.6k • written 13 months ago by
Xiao
• 0
2
votes
4
replies
1.3k
views
Correct the batch effect in methylation analysis in R
BatchEffect
limma
methylationArrayAnalysis
updated 14 months ago by
Gordon Smyth
52k • written 14 months ago by
kyj2226
• 0
1
vote
4
replies
1.0k
views
controling for batch effect while preserving variation within repeated measures that unevenly distributed across batches
miRNA
BatchEffect
RNASeq
limma
15 months ago
Wending
• 0
0
votes
4
replies
1.0k
views
How to correct for known and surrogate variables in DESeq2?
DESeq2
BatchEffect
sva
limma
updated 9 months ago by
Michael Love
43k • written 15 months ago by
Crystal571
• 0
0
votes
1
reply
690
views
Batch effect adjust in model matrix
BatchEffect
edgeR
updated 16 months ago by
ATpoint
★ 4.6k • written 16 months ago by
Giuseppe
• 0
3
votes
5
replies
1.6k
views
Getting batch corrected counts after RUVSeq
BatchEffect
RUVSeq
RNASeq
DESeq2
updated 16 months ago by
ATpoint
★ 4.6k • written 17 months ago by
Shashank
• 0
2
votes
5
replies
2.2k
views
removing the batch effect for vst counts and defining the batches in removeBatchEffect function
DESeq2
BatchEffect
limma
updated 18 months ago by
Gordon Smyth
52k • written 18 months ago by
Sara
• 0
2
votes
3
replies
2.2k
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 18 months ago by
James W. MacDonald
67k • written 18 months ago by
D-Bug
▴ 10
3
votes
4
replies
1.4k
views
lfcShrink() and batch effects in DESeq2
BatchEffect
lfcshrink
RNA-seq
DESeq2
18 months ago
Eva
▴ 10
0
votes
2
replies
928
views
smallRNA-seq analysis batch correction in limma
BatchEffect
limma
18 months ago
Eleonora
• 0
1
vote
1
reply
665
views
Best way to handle batch effects from difference Mice?
RNASeqData
BatchEffect
edgeR
limma
updated 19 months ago by
Gordon Smyth
52k • written 19 months ago by
Sara
• 0
2
votes
3
replies
2.0k
views
PCA for QC should include subset of top variable genes or full set of genes in RNAseq data?
BatchQC
RNASeqData
sva
BatchEffect
updated 19 months ago by
ATpoint
★ 4.6k • written 19 months ago by
amnahsiddiqa
▴ 10
0
votes
0
replies
624
views
How to go for Batch correction in RNA-seq expeiment conducted based on imbalanced Experimental design ?
RNASeqData
BatchEffect
sva
19 months ago
amnahsiddiqa
▴ 10
1
vote
1
reply
737
views
WGCNA Cluster batch effect
BatchEffect
TCGA
WGCNA
updated 19 months ago by
ATpoint
★ 4.6k • written 19 months ago by
khaserdene99
• 0
2
votes
5
replies
1.8k
views
DESeq2 remove batch effect
BatchEffect
RNASeqData
WGCNA
DESeq2
updated 9 months ago by
Ashley
• 0 • written 20 months ago by
zxc741xb
• 0
1
vote
2
replies
1.5k
views
Batch effect between biological replicates
BatchEffect
DESeq2
21 months ago • updated 20 months ago
gtechbio
▴ 10
0
votes
4
replies
1.4k
views
Combine RNA-seq
BatchEffect
R
rnaseq
updated 21 months ago by
swbarnes2
★ 1.4k • written 21 months ago by
Young Tae
• 0
2
votes
4
replies
2.1k
views
How to get TPM / FPKM after batch correction with DESeq2?
DESeq2
BatchEffect
tpm
fpkm
21 months ago
vk
• 0
2
votes
2
replies
1.4k
views
Error in checkFullRank(modelMatrix)
DESeq2
BatchEffect
DifferentialExpression
updated 22 months ago by
ATpoint
★ 4.6k • written 22 months ago by
AZ
▴ 30
2
votes
3
replies
1.4k
views
Batch correction and Deseq2
DESeq2
WGCNA
Normalization
NormalyzerDE
BatchEffect
updated 22 months ago by
ATpoint
★ 4.6k • written 23 months ago by
suphamon.j
▴ 20
2
votes
1
reply
963
views
How to identify the batch informations from the sample ID?
TCGAbiolinks
BatchQC
BatchEffect
updated 17 months ago by
wrab425
• 0 • written 23 months ago by
snijesh
▴ 200
3
votes
2
replies
1.1k
views
Batch question Bulk RNA-Seq
BatchEffect
RNASeq
23 months ago
chf
• 0
2
votes
1
reply
2.5k
views
DESeq2 design after combatseq batch correction
DESeq2
BatchEffect
updated 23 months ago by
ATpoint
★ 4.6k • written 23 months ago by
Tyroone
• 0
0
votes
1
reply
653
views
Analysis with Batch correction
DESeq2
BatchEffect
updated 23 months ago by
Michael Love
43k • written 23 months ago by
giulia.lopatriello
• 0
1
vote
1
reply
1.1k
views
Batch effect: Is it correct to put ~0 preparing the model.matrix to remove batch effect?
edgeR
model.matrix
BatchEffect
updated 23 months ago by
James W. MacDonald
67k • written 23 months ago by
greta
• 0
5
votes
2
replies
1.1k
views
Sva and batch effect
limma
BatchEffect
sva
updated 2.0 years ago by
Gordon Smyth
52k • written 2.0 years ago by
Lenny186
• 0
1
vote
1
reply
3.4k
views
batch effect correction before DESeq2 analysis
DESeq2
BatchEffect
updated 2.0 years ago by
ATpoint
★ 4.6k • written 2.0 years ago by
luca.s
▴ 50
0
votes
0
replies
1.1k
views
Trying to use a NanoString expression set with batch effects to do GSVA
GSVA
Normalization
BatchEffect
GSVAdata
NanoString
2.1 years ago
Zhijie
• 0
1
vote
0
replies
990
views
Use scran's normalization by deconvolution for each individual sample or over all samples
scran
Normalization
scRNA
BatchEffect
2.1 years ago
r_grau
▴ 10
50 results • Page
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Recent ...
Replies
Comment: displaying the differential expression with deseq2 over 4X2 samples with the in
by
Martijn
• 0
thanks James, but if I do pairwise analyses per subject, I get the impression that I only get the intercepts per gene. Do you mean regardin…
Comment: plyranges: find exact GRanges match keeping metadata columns
by
alexis.weinreb
• 0
Thank you, this does clarify the available options.
Answer: displaying the differential expression with deseq2 over 4X2 samples with the in
by
James W. MacDonald
67k
If you have paired data you should block on subject, which is algebraically the same as fitting a model on the difference between treated a…
Answer: How to compare expression levels of genes between scRNAseq and bulkRNAseq?
by
jodan
• 0
Your approach sounds solid! You might also consider plotting a scatter plot comparing log2 fold changes from both datasets to identify gene…
Answer: Unused arguments error without used arguments in GSVA?
by
jodan
• 0
It looks like the ssgseaParam function might not be passing the correct parameters to GSVA::gsva(). The error suggests that minSize and max…
Votes
Answer: Find exact GRanges match keeping metadata columns
Answer: Find exact GRanges match keeping metadata columns
Answer: Unused arguments error without used arguments in GSVA?
Answer: Unused arguments error without used arguments in GSVA?
Answer: Unused arguments error without used arguments in GSVA?
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