Showing : BatchEffect • reset
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Batch correction for microarray
BatchEffect sva MicroarrayData
3 days ago Shaimaa Gamal • 0
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5
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417
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Is there a way to do DEG analysis across two batches sharing one sample only?
DESeq2 DifferentialExpression RNASeqData BatchEffect
written 3 months ago by • 0
2
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9
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1.2k
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Why did PCA plots look exactly the same after adjusting for batch covariate in DESeq2 design?
DESeq2 BatchEffect
3 months ago Quang NN ▴ 10
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4
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2.0k
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Differential Expression Analysis with unbalanced batches without replication between conditions
edgeR BatchEffect
updated 5 months ago by 52k • written 5 months ago by • 0
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2
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825
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Integration of Single Cell Experiments with batchelor::fastMNN
fastMNN SingleCellData BatchEffect batchelor
6 months ago José • 0
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6
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1.1k
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[DESeq2] Introduce a bias in DESeq2
DifferentialExpression DESeq2 BatchEffect
updated 5 months ago by 43k • written 6 months ago by • 0
5
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4
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737
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How to control batch effect if Group and batch are same?
limma DESeq2 BatchEffect
updated 6 months ago by ★ 4.8k • written 6 months ago by • 0
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5
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982
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heatmap with batch effect
DESeq2 BatchEffect
6 months ago tothuhien • 0
2
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2
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526
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Batch adjustment for cohort based RNA seq data
RNASeqPower removeBatchEffect cpm Batcheffect
7 months ago sukeshinik5 ▴ 20
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2
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516
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ReactomeGSA adjustment for confounding variables
BiologicalQuestion ReactomeGSA BatchEffect
written 7 months ago by • 0
4
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7
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1.7k
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What does evidence of batch effect in bulk rnaseq look like?
surrogatevariables DESeq2 BatchEffect bulkrna-seq sva-seq
updated 8 months ago by ▴ 10 • written 9 months ago by ▴ 70
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2
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684
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Control group between 2 batches have different expression in RNAseq data
BatchQC BatchEffect rnaseqGene Normalization
updated 10 months ago by ▴ 10 • written 11 months ago by • 0
2
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2
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796
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How to remove batch effect to combine RNAseq data from 2 different experiments?
BatchQC BatchEffect RNASeq
updated 10 months ago by ▴ 10 • written 11 months ago by • 0
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1
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482
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ReactomeGSA for RNASeq
ReactomeGSA BatchEffect RNASeqData
updated 7 months ago by ▴ 20 • written 11 months ago by • 0
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2
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1.6k
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Batch effect correction: methylome data
sesame BatchEffect MethylationArray
updated 11 months ago by ▴ 20 • written 11 months ago by • 0
2
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9
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1.4k
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Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2 RUVSeq RUVseq BatchEffect DES
updated 12 months ago by 68k • written 12 months ago by • 0
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2
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878
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RNAseq:Technical replicates from different batches
technicalReplicates BatchEffect limma RNASeq
12 months ago catv • 0
0
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8
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1.1k
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DESeq and SVA for batch effect
DESeq2 BatchEffect sva
13 months ago michelafrancesconi8 • 0
1
vote
3
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850
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DESEQ2 Batch Effect
DESeq2 BatchEffect RNASeq
updated 13 months ago by ★ 1.4k • written 13 months ago by ▴ 10
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465
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Can I combine collinear variables into a single value
BatchEffect limma
13 months ago Harrsha • 0
2
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1
reply
597
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Limma Question
DESeq2 BatchEffect limma RNASeq
updated 14 months ago by 43k • written 14 months ago by ▴ 10
4
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1
reply
1.5k
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When should I correct for batch effects
BatchEffect SingleCellExperiment
updated 15 months ago by 68k • written 15 months ago by ▴ 20
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5
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1.6k
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Can SVs identified from sva be used for removeBatchEffect() in DESeq2
sva DESeq2 BatchEffect limma
updated 15 months ago by ★ 4.8k • written 15 months ago by • 0
2
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4
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1.5k
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Correct the batch effect in methylation analysis in R
BatchEffect limma methylationArrayAnalysis
updated 16 months ago by 52k • written 16 months ago by • 0
1
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4
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1.2k
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controling for batch effect while preserving variation within repeated measures that unevenly distributed across batches
miRNA BatchEffect RNASeq limma
17 months ago Wending • 0
0
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4
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1.2k
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How to correct for known and surrogate variables in DESeq2?
DESeq2 BatchEffect sva limma
updated 12 months ago by 43k • written 18 months ago by • 0
0
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1
reply
727
views
Batch effect adjust in model matrix
BatchEffect edgeR
updated 19 months ago by ★ 4.8k • written 19 months ago by • 0
3
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5
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1.8k
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Getting batch corrected counts after RUVSeq
BatchEffect RUVSeq RNASeq DESeq2
updated 19 months ago by ★ 4.8k • written 19 months ago by • 0
2
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5
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2.4k
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removing the batch effect for vst counts and defining the batches in removeBatchEffect function
DESeq2 BatchEffect limma
updated 20 months ago by 52k • written 20 months ago by • 0
2
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3
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2.6k
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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 20 months ago by 68k • written 20 months ago by ▴ 10
3
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4
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1.6k
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lfcShrink() and batch effects in DESeq2
BatchEffect lfcshrink RNA-seq DESeq2
20 months ago Eva ▴ 10
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2
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1.0k
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smallRNA-seq analysis batch correction in limma
BatchEffect limma
21 months ago Eleonora • 0
1
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1
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705
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Best way to handle batch effects from difference Mice?
RNASeqData BatchEffect edgeR limma
updated 21 months ago by 52k • written 21 months ago by • 0
2
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3
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2.3k
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PCA for QC should include subset of top variable genes or full set of genes in RNAseq data?
BatchQC RNASeqData sva BatchEffect
updated 22 months ago by ★ 4.8k • written 22 months ago by ▴ 10
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0
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683
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How to go for Batch correction in RNA-seq expeiment conducted based on imbalanced Experimental design ?
RNASeqData BatchEffect sva
22 months ago amnahsiddiqa ▴ 10
1
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1
reply
788
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WGCNA Cluster batch effect
BatchEffect TCGA WGCNA
updated 22 months ago by ★ 4.8k • written 22 months ago by • 0
2
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5
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2.0k
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DESeq2 remove batch effect
BatchEffect RNASeqData WGCNA DESeq2
updated 12 months ago by • 0 • written 22 months ago by • 0
1
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2
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1.6k
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Batch effect between biological replicates
BatchEffect DESeq2
23 months ago gtechbio ▴ 10
0
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4
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1.5k
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Combine RNA-seq
BatchEffect R rnaseq
updated 2.0 years ago by ★ 1.4k • written 2.0 years ago by • 0
2
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4
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2.2k
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How to get TPM / FPKM after batch correction with DESeq2?
DESeq2 BatchEffect tpm fpkm
2.0 years ago vk • 0
2
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2
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1.5k
views
Error in checkFullRank(modelMatrix)
DESeq2 BatchEffect DifferentialExpression
updated 2.0 years ago by ★ 4.8k • written 2.0 years ago by ▴ 30
2
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3
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1.5k
views
Batch correction and Deseq2
DESeq2 WGCNA Normalization NormalyzerDE BatchEffect
updated 2.1 years ago by ★ 4.8k • written 2.1 years ago by ▴ 20
2
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1
reply
1.1k
views
How to identify the batch informations from the sample ID?
TCGAbiolinks BatchQC BatchEffect
updated 20 months ago by • 0 • written 2.1 years ago by ▴ 200
3
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2
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1.3k
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Batch question Bulk RNA-Seq
BatchEffect RNASeq
2.1 years ago chf • 0
2
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1
reply
2.9k
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DESeq2 design after combatseq batch correction
DESeq2 BatchEffect
updated 2.2 years ago by ★ 4.8k • written 2.2 years ago by • 0
0
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1
reply
696
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Analysis with Batch correction
DESeq2 BatchEffect
updated 2.2 years ago by 43k • written 2.2 years ago by • 0
1
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1
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1.2k
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Batch effect: Is it correct to put ~0 preparing the model.matrix to remove batch effect?
edgeR model.matrix BatchEffect
updated 2.2 years ago by 68k • written 2.2 years ago by • 0
5
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2
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1.2k
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Sva and batch effect
limma BatchEffect sva
updated 2.2 years ago by 52k • written 2.2 years ago by • 0
1
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1
reply
4.2k
views
batch effect correction before DESeq2 analysis
DESeq2 BatchEffect
updated 2.2 years ago by ★ 4.8k • written 2.2 years ago by ▴ 50
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0
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1.2k
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Trying to use a NanoString expression set with batch effects to do GSVA
GSVA Normalization BatchEffect GSVAdata NanoString
2.3 years ago Zhijie • 0
50 results • Page 1 of 1
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Comment: RNA Seq using Lrt by Rob • 0
So if I have understood what you have said : If i want to see if Day (time) has an effect / is being tested - then the reduced model should…
Comment: How to convert transcript counts to gene counts in R? by ben • 0
Simply summing transcripts by gene is sufficient for use with DESeq2. [sprunki clicker][1] [1]: https://sprunkiclicker.com/
Answer: EuroBioC2024 abstract submission is open! by Ali • 0
[Promo products][1] are a smart way to boost visibility, especially with exciting updates like *News: EuroBioC2024 abstract submission is o…
Answer: ROAST for small sets by Gordon Smyth 52k
The p-values from `mroast` will be the same (up to sampling variability associated with random rotations) regardless of whether you test al…
Comment: FlowSOM library requires igraph but igraph does not install by Szabolcs • 0
The R/igraph Installation FAQ covers most issues: https://r.igraph.org/articles/installation-troubleshooting.html
Votes
Answer: ROAST for small sets
Answer: ROAST for small sets
A: conceptual question about FDR, FDR adjusted p-value and q-value
Comment: edgeR::cpm() results in negative values from raw counts of 0
Comment: edgeR::cpm() results in negative values from raw counts of 0
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