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Batcheffect
•
reset
0
votes
0
replies
314
views
Batch correction for microarray
BatchEffect
sva
MicroarrayData
6 months ago
Shaimaa Gamal
• 0
0
votes
5
replies
678
views
Is there a way to do DEG analysis across two batches sharing one sample only?
DESeq2
DifferentialExpression
RNASeqData
BatchEffect
written 9 months ago by
georgeyu703
• 0
2
votes
9
replies
1.6k
views
Why did PCA plots look exactly the same after adjusting for batch covariate in DESeq2 design?
DESeq2
BatchEffect
9 months ago
Quang NN
▴ 10
2
votes
4
replies
2.4k
views
Differential Expression Analysis with unbalanced batches without replication between conditions
edgeR
BatchEffect
updated 11 months ago by
Gordon Smyth
53k • written 11 months ago by
Thili
• 0
0
votes
2
replies
1.1k
views
Integration of Single Cell Experiments with batchelor::fastMNN
fastMNN
SingleCellData
BatchEffect
batchelor
12 months ago
José
• 0
0
votes
6
replies
1.4k
views
[DESeq2] Introduce a bias in DESeq2
DifferentialExpression
DESeq2
BatchEffect
updated 12 months ago by
Michael Love
43k • written 12 months ago by
CriticalPeriod
• 0
5
votes
4
replies
966
views
How to control batch effect if Group and batch are same?
limma
DESeq2
BatchEffect
updated 12 months ago by
ATpoint
★ 5.0k • written 13 months ago by
Bioinformagician
• 0
1
vote
6
replies
1.4k
views
heatmap with batch effect
DESeq2
BatchEffect
written 13 months ago by
tothuhien
• 0
2
votes
2
replies
723
views
Batch adjustment for cohort based RNA seq data
RNASeqPower
removeBatchEffect
cpm
Batcheffect
13 months ago
sukeshinik5
▴ 20
0
votes
2
replies
688
views
ReactomeGSA adjustment for confounding variables
BiologicalQuestion
ReactomeGSA
BatchEffect
written 14 months ago by
Shaimaa Gamal
• 0
4
votes
7
replies
2.1k
views
What does evidence of batch effect in bulk rnaseq look like?
surrogatevariables
DESeq2
BatchEffect
bulkrna-seq
sva-seq
updated 15 months ago by
jessica.anderson
▴ 10 • written 16 months ago by
BioinfGuru
▴ 70
2
votes
2
replies
848
views
Control group between 2 batches have different expression in RNAseq data
BatchQC
BatchEffect
rnaseqGene
Normalization
updated 17 months ago by
jessica.anderson
▴ 10 • written 17 months ago by
Đình Vinh
• 0
2
votes
2
replies
993
views
How to remove batch effect to combine RNAseq data from 2 different experiments?
BatchQC
BatchEffect
RNASeq
updated 17 months ago by
jessica.anderson
▴ 10 • written 17 months ago by
ttt
• 0
0
votes
1
reply
674
views
ReactomeGSA for RNASeq
ReactomeGSA
BatchEffect
RNASeqData
updated 14 months ago by
jg
▴ 20 • written 17 months ago by
Shaimaa Gamal
• 0
0
votes
2
replies
2.1k
views
Batch effect correction: methylome data
sesame
BatchEffect
MethylationArray
updated 17 months ago by
zhouwanding
▴ 20 • written 17 months ago by
Seungmin
• 0
2
votes
9
replies
1.7k
views
Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2
RUVSeq
RUVseq
BatchEffect
DES
updated 18 months ago by
James W. MacDonald
68k • written 18 months ago by
Alexandre
• 0
0
votes
2
replies
1.2k
views
RNAseq:Technical replicates from different batches
technicalReplicates
BatchEffect
limma
RNASeq
18 months ago
catv
• 0
0
votes
8
replies
1.5k
views
DESeq and SVA for batch effect
DESeq2
BatchEffect
sva
20 months ago
michelafrancesconi8
• 0
1
vote
3
replies
1.0k
views
DESEQ2 Batch Effect
DESeq2
BatchEffect
RNASeq
updated 20 months ago by
swbarnes2
★ 1.4k • written 20 months ago by
sap275
▴ 10
0
votes
0
replies
573
views
Can I combine collinear variables into a single value
BatchEffect
limma
20 months ago
Harrsha
• 0
2
votes
1
reply
724
views
Limma Question
DESeq2
BatchEffect
limma
RNASeq
updated 20 months ago by
Michael Love
43k • written 20 months ago by
sap275
▴ 10
4
votes
1
reply
1.8k
views
When should I correct for batch effects
BatchEffect
SingleCellExperiment
updated 21 months ago by
James W. MacDonald
68k • written 21 months ago by
NeuroDaniel
▴ 20
0
votes
5
replies
1.9k
views
Can SVs identified from sva be used for removeBatchEffect() in DESeq2
sva
DESeq2
BatchEffect
limma
updated 22 months ago by
ATpoint
★ 5.0k • written 22 months ago by
Xiao
• 0
2
votes
4
replies
1.7k
views
Correct the batch effect in methylation analysis in R
BatchEffect
limma
methylationArrayAnalysis
updated 22 months ago by
Gordon Smyth
53k • written 23 months ago by
kyj2226
• 0
1
vote
4
replies
1.5k
views
controling for batch effect while preserving variation within repeated measures that unevenly distributed across batches
miRNA
BatchEffect
RNASeq
limma
24 months ago
Wending
• 0
0
votes
4
replies
1.4k
views
How to correct for known and surrogate variables in DESeq2?
DESeq2
BatchEffect
sva
limma
updated 18 months ago by
Michael Love
43k • written 2.0 years ago by
Crystal571
• 0
0
votes
1
reply
835
views
Batch effect adjust in model matrix
BatchEffect
edgeR
updated 2.1 years ago by
ATpoint
★ 5.0k • written 2.1 years ago by
Giuseppe
• 0
3
votes
5
replies
2.1k
views
Getting batch corrected counts after RUVSeq
BatchEffect
RUVSeq
RNASeq
DESeq2
updated 2.1 years ago by
ATpoint
★ 5.0k • written 2.1 years ago by
Shashank
• 0
2
votes
5
replies
2.8k
views
removing the batch effect for vst counts and defining the batches in removeBatchEffect function
DESeq2
BatchEffect
limma
updated 2.2 years ago by
Gordon Smyth
53k • written 2.2 years ago by
Sara
• 0
2
votes
3
replies
3.0k
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 2.2 years ago by
James W. MacDonald
68k • written 2.2 years ago by
D-Bug
▴ 10
3
votes
4
replies
2.0k
views
lfcShrink() and batch effects in DESeq2
BatchEffect
lfcshrink
RNA-seq
DESeq2
2.2 years ago
Eva
▴ 10
0
votes
2
replies
1.2k
views
smallRNA-seq analysis batch correction in limma
BatchEffect
limma
2.3 years ago
Eleonora
• 0
1
vote
1
reply
796
views
Best way to handle batch effects from difference Mice?
RNASeqData
BatchEffect
edgeR
limma
updated 2.3 years ago by
Gordon Smyth
53k • written 2.3 years ago by
Sara
• 0
2
votes
3
replies
2.5k
views
PCA for QC should include subset of top variable genes or full set of genes in RNAseq data?
BatchQC
RNASeqData
sva
BatchEffect
updated 2.3 years ago by
ATpoint
★ 5.0k • written 2.3 years ago by
amnahsiddiqa
▴ 10
0
votes
0
replies
854
views
How to go for Batch correction in RNA-seq expeiment conducted based on imbalanced Experimental design ?
RNASeqData
BatchEffect
sva
2.3 years ago
amnahsiddiqa
▴ 10
1
vote
1
reply
925
views
WGCNA Cluster batch effect
BatchEffect
TCGA
WGCNA
updated 2.3 years ago by
ATpoint
★ 5.0k • written 2.3 years ago by
khaserdene99
• 0
2
votes
5
replies
2.3k
views
DESeq2 remove batch effect
BatchEffect
RNASeqData
WGCNA
DESeq2
updated 18 months ago by
Ashley
• 0 • written 2.4 years ago by
zxc741xb
• 0
1
vote
2
replies
1.8k
views
Batch effect between biological replicates
BatchEffect
DESeq2
2.5 years ago
gtechbio
▴ 10
0
votes
4
replies
1.7k
views
Combine RNA-seq
BatchEffect
R
rnaseq
updated 2.5 years ago by
swbarnes2
★ 1.4k • written 2.5 years ago by
Young Tae
• 0
2
votes
4
replies
2.5k
views
How to get TPM / FPKM after batch correction with DESeq2?
DESeq2
BatchEffect
tpm
fpkm
2.5 years ago
vk
• 0
2
votes
2
replies
1.7k
views
Error in checkFullRank(modelMatrix)
DESeq2
BatchEffect
DifferentialExpression
updated 2.5 years ago by
ATpoint
★ 5.0k • written 2.5 years ago by
AZ
▴ 30
2
votes
3
replies
1.7k
views
Batch correction and Deseq2
DESeq2
WGCNA
Normalization
NormalyzerDE
BatchEffect
updated 2.6 years ago by
ATpoint
★ 5.0k • written 2.6 years ago by
suphamon.j
▴ 20
2
votes
1
reply
1.3k
views
How to identify the batch informations from the sample ID?
TCGAbiolinks
BatchQC
BatchEffect
updated 2.2 years ago by
wrab425
• 0 • written 2.6 years ago by
snijesh
▴ 200
3
votes
2
replies
1.5k
views
Batch question Bulk RNA-Seq
BatchEffect
RNASeq
2.6 years ago
chf
• 0
2
votes
1
reply
3.2k
views
DESeq2 design after combatseq batch correction
DESeq2
BatchEffect
updated 2.7 years ago by
ATpoint
★ 5.0k • written 2.7 years ago by
Tyroone
• 0
0
votes
1
reply
783
views
Analysis with Batch correction
DESeq2
BatchEffect
updated 2.7 years ago by
Michael Love
43k • written 2.7 years ago by
giulia.lopatriello
• 0
1
vote
1
reply
1.3k
views
Batch effect: Is it correct to put ~0 preparing the model.matrix to remove batch effect?
edgeR
model.matrix
BatchEffect
updated 2.7 years ago by
James W. MacDonald
68k • written 2.7 years ago by
greta
• 0
5
votes
2
replies
1.3k
views
Sva and batch effect
limma
BatchEffect
sva
updated 2.7 years ago by
Gordon Smyth
53k • written 2.7 years ago by
Lenny186
• 0
1
vote
1
reply
4.7k
views
batch effect correction before DESeq2 analysis
DESeq2
BatchEffect
updated 2.8 years ago by
ATpoint
★ 5.0k • written 2.8 years ago by
luca.s
▴ 50
0
votes
0
replies
1.4k
views
Trying to use a NanoString expression set with batch effects to do GSVA
GSVA
Normalization
BatchEffect
GSVAdata
NanoString
2.8 years ago
Zhijie
• 0
93 results • Page
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Replies
Comment: "Watched Tags" are being erased rather than updated
by
shepherl
4.2k
I can reproduce this and have opened an issue on the code base https://github.com/Bioconductor/support.bioconductor.org/issues/112
Comment: "Watched Tags" are being erased rather than updated
by
shepherl
4.2k
we can investigate this issue. thank you for bringing it to our attention
Comment: deseq2 filter the low counts
by
Michael Love
43k
> But within each comparison (contrast), if I trace some DEGs back to the original salmon merged gene counts (or even to normalised counts)…
Comment: deseq2 filter the low counts
by
empty_mt
• 0
Thank you for you suggestion to look at the pre-filtering section in the DESeq2 vignettes - am I missing something? I have 6 treatments, …
Comment: deseq2 filter the low counts
by
Michael Love
43k
Have you seen this part: https://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#pre-filtering
Votes
Comment: "Watched Tags" are being erased rather than updated
Comment: deseq2 filter the low counts
Answer: DESeq2 interactions
Answer: Important: Bioconductor Release 3.22 Delayed
A: Multi-level experiments in Limma
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