Showing : batcheffect • reset
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Batch correction for microarray
BatchEffect sva MicroarrayData
10 months ago Shaimaa Gamal • 0
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5
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863
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Is there a way to do DEG analysis across two batches sharing one sample only?
DESeq2 DifferentialExpression RNASeqData BatchEffect
written 13 months ago by • 0
2
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9
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2.3k
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Why did PCA plots look exactly the same after adjusting for batch covariate in DESeq2 design?
DESeq2 BatchEffect
14 months ago • updated 13 months ago Quang NN ▴ 10
2
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4
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3.1k
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Differential Expression Analysis with unbalanced batches without replication between conditions
edgeR BatchEffect
updated 16 months ago by 53k • written 16 months ago by • 0
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2
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1.8k
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Integration of Single Cell Experiments with batchelor::fastMNN
fastMNN SingleCellData BatchEffect batchelor
16 months ago José • 0
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6
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1.6k
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[DESeq2] Introduce a bias in DESeq2
DifferentialExpression DESeq2 BatchEffect
updated 16 months ago by 43k • written 17 months ago by • 0
5
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4
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1.2k
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How to control batch effect if Group and batch are same?
limma DESeq2 BatchEffect
updated 17 months ago by ★ 5.0k • written 17 months ago by • 0
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6
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1.7k
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heatmap with batch effect
DESeq2 BatchEffect
written 17 months ago by • 0
2
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2
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884
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Batch adjustment for cohort based RNA seq data
RNASeqPower removeBatchEffect cpm Batcheffect
17 months ago sukeshinik5 ▴ 20
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2
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795
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ReactomeGSA adjustment for confounding variables
BiologicalQuestion ReactomeGSA BatchEffect
written 18 months ago by • 0
4
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7
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3.0k
views
What does evidence of batch effect in bulk rnaseq look like?
surrogatevariables DESeq2 BatchEffect bulkrna-seq sva-seq
updated 19 months ago by ▴ 10 • written 20 months ago by ▴ 70
2
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2
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1.0k
views
Control group between 2 batches have different expression in RNAseq data
BatchQC BatchEffect rnaseqGene Normalization
updated 21 months ago by ▴ 10 • written 22 months ago by • 0
2
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2
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1.2k
views
How to remove batch effect to combine RNAseq data from 2 different experiments?
BatchQC BatchEffect RNASeq
updated 21 months ago by ▴ 10 • written 22 months ago by • 0
0
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1
reply
838
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ReactomeGSA for RNASeq
ReactomeGSA BatchEffect RNASeqData
updated 18 months ago by ▴ 20 • written 22 months ago by • 0
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2
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2.9k
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Batch effect correction: methylome data
sesame BatchEffect MethylationArray
updated 22 months ago by ▴ 20 • written 22 months ago by • 0
2
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9
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2.1k
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Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2 RUVSeq RUVseq BatchEffect DES
updated 22 months ago by 68k • written 22 months ago by • 0
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2
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1.5k
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RNAseq:Technical replicates from different batches
technicalReplicates BatchEffect limma RNASeq
23 months ago catv • 0
0
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8
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1.8k
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DESeq and SVA for batch effect
DESeq2 BatchEffect sva
2.0 years ago michelafrancesconi8 • 0
1
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3
replies
1.2k
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DESEQ2 Batch Effect
DESeq2 BatchEffect RNASeq
updated 2.0 years ago by ★ 1.4k • written 2.0 years ago by ▴ 10
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0
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641
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Can I combine collinear variables into a single value
BatchEffect limma
2.0 years ago Harrsha • 0
2
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1
reply
834
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Limma Question
DESeq2 BatchEffect limma RNASeq
updated 2.0 years ago by 43k • written 2.0 years ago by ▴ 10
4
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1
reply
2.2k
views
When should I correct for batch effects
BatchEffect SingleCellExperiment
updated 2.1 years ago by 68k • written 2.1 years ago by ▴ 20
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5
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2.2k
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Can SVs identified from sva be used for removeBatchEffect() in DESeq2
sva DESeq2 BatchEffect limma
updated 2.2 years ago by ★ 5.0k • written 2.2 years ago by • 0
2
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4
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2.1k
views
Correct the batch effect in methylation analysis in R
BatchEffect limma methylationArrayAnalysis
updated 2.3 years ago by 53k • written 2.3 years ago by • 0
1
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4
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1.8k
views
controling for batch effect while preserving variation within repeated measures that unevenly distributed across batches
miRNA BatchEffect RNASeq limma
2.4 years ago Wending • 0
0
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4
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1.6k
views
How to correct for known and surrogate variables in DESeq2?
DESeq2 BatchEffect sva limma
updated 23 months ago by 43k • written 2.4 years ago by • 0
0
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1
reply
931
views
Batch effect adjust in model matrix
BatchEffect edgeR
updated 2.5 years ago by ★ 5.0k • written 2.5 years ago by • 0
3
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5
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2.4k
views
Getting batch corrected counts after RUVSeq
BatchEffect RUVSeq RNASeq DESeq2
updated 2.5 years ago by ★ 5.0k • written 2.5 years ago by • 0
2
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5
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3.5k
views
removing the batch effect for vst counts and defining the batches in removeBatchEffect function
DESeq2 BatchEffect limma
updated 2.6 years ago by 53k • written 2.6 years ago by • 0
2
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3
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3.4k
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 2.6 years ago by 68k • written 2.6 years ago by ▴ 10
3
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4
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2.8k
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lfcShrink() and batch effects in DESeq2
BatchEffect lfcshrink RNA-seq DESeq2
2.6 years ago Eva ▴ 30
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2
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1.3k
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smallRNA-seq analysis batch correction in limma
BatchEffect limma
2.7 years ago Eleonora • 0
1
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1
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887
views
Best way to handle batch effects from difference Mice?
RNASeqData BatchEffect edgeR limma
updated 2.7 years ago by 53k • written 2.7 years ago by • 0
2
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3
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3.0k
views
PCA for QC should include subset of top variable genes or full set of genes in RNAseq data?
BatchQC RNASeqData sva BatchEffect
updated 2.7 years ago by ★ 5.0k • written 2.7 years ago by ▴ 10
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0
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956
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How to go for Batch correction in RNA-seq expeiment conducted based on imbalanced Experimental design ?
RNASeqData BatchEffect sva
2.7 years ago amnahsiddiqa ▴ 10
1
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1
reply
1.0k
views
WGCNA Cluster batch effect
BatchEffect TCGA WGCNA
updated 2.7 years ago by ★ 5.0k • written 2.7 years ago by • 0
2
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5
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2.6k
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DESeq2 remove batch effect
BatchEffect RNASeqData WGCNA DESeq2
updated 23 months ago by • 0 • written 2.8 years ago by • 0
1
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2
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2.0k
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Batch effect between biological replicates
BatchEffect DESeq2
2.8 years ago gtechbio ▴ 10
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4
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1.9k
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Combine RNA-seq
BatchEffect R rnaseq
updated 2.9 years ago by ★ 1.4k • written 2.9 years ago by • 0
2
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4
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2.7k
views
How to get TPM / FPKM after batch correction with DESeq2?
DESeq2 BatchEffect tpm fpkm
2.9 years ago vk • 0
2
votes
2
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1.9k
views
Error in checkFullRank(modelMatrix)
DESeq2 BatchEffect DifferentialExpression
updated 2.9 years ago by ★ 5.0k • written 2.9 years ago by ▴ 20
2
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3
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2.0k
views
Batch correction and Deseq2
DESeq2 WGCNA Normalization NormalyzerDE BatchEffect
updated 3.0 years ago by ★ 5.0k • written 3.0 years ago by ▴ 20
2
votes
1
reply
1.6k
views
How to identify the batch informations from the sample ID?
TCGAbiolinks BatchQC BatchEffect
updated 2.6 years ago by • 0 • written 3.0 years ago by ▴ 200
3
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2
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1.6k
views
Batch question Bulk RNA-Seq
BatchEffect RNASeq
3.0 years ago chf • 0
2
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1
reply
3.6k
views
DESeq2 design after combatseq batch correction
DESeq2 BatchEffect
updated 3.1 years ago by ★ 5.0k • written 3.1 years ago by • 0
0
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1
reply
868
views
Analysis with Batch correction
DESeq2 BatchEffect
updated 3.1 years ago by 43k • written 3.1 years ago by • 0
1
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1
reply
1.5k
views
Batch effect: Is it correct to put ~0 preparing the model.matrix to remove batch effect?
edgeR model.matrix BatchEffect
updated 3.1 years ago by 68k • written 3.1 years ago by • 0
5
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2
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1.5k
views
Sva and batch effect
limma BatchEffect sva
updated 3.1 years ago by 53k • written 3.1 years ago by • 0
1
vote
1
reply
5.6k
views
batch effect correction before DESeq2 analysis
DESeq2 BatchEffect
updated 3.1 years ago by ★ 5.0k • written 3.1 years ago by ▴ 50
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0
replies
1.5k
views
Trying to use a NanoString expression set with batch effects to do GSVA
GSVA Normalization BatchEffect GSVAdata NanoString
3.2 years ago Zhijie • 0
93 results • Page 1 of 2
Recent ...
Replies
Answer: Is it still possible to do batch correction for my data? by Gordon Smyth 53k
I agree with the comments from James MacDonald, but I will add that if you use the standard linear model correction for batch ``` design <-…
Answer: specifying refColumn in calcNormFactors() by Gordon Smyth 53k
Your question is about cross-validation rather than specifically about edgeR. A general principle of cross-validation is that you must norm…
Answer: Sex prediction in sesame for EPICV2 by Tim Peters ▴ 230
Hi Pooja, There is a tutorial for preprocessing EPICv2 via sesame here: https://clark-lab.github.io/EPICv2_tutorial/. There is no call t…
Comment: Convergence Issues and Model Selection DESeq2 by dani.guan.3 • 0
Thank you, I appreciate your time and help.
Comment: Convergence Issues and Model Selection DESeq2 by Michael Love 43k
> out of my 30,229 genes, 795 (2.6%) are better explained ... Not exactly. Frequentist statistics is not symmetric in this way. If it were…
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DiffBind dropping peaks in ATAC-seq data
A: decideTests() options in LIMMA
A: Removing cell cycle genes in large data set integration
A: Removing cell cycle genes in large data set integration
Answer: Quick two questions on limpa
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