Showing : Batcheffect • reset
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Batch correction for microarray
BatchEffect sva MicroarrayData
7 months ago Shaimaa Gamal • 0
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5
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722
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Is there a way to do DEG analysis across two batches sharing one sample only?
DESeq2 DifferentialExpression RNASeqData BatchEffect
written 10 months ago by • 0
2
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9
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1.7k
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Why did PCA plots look exactly the same after adjusting for batch covariate in DESeq2 design?
DESeq2 BatchEffect
11 months ago • updated 10 months ago Quang NN ▴ 10
2
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4
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2.5k
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Differential Expression Analysis with unbalanced batches without replication between conditions
edgeR BatchEffect
updated 13 months ago by 53k • written 13 months ago by • 0
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2
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1.1k
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Integration of Single Cell Experiments with batchelor::fastMNN
fastMNN SingleCellData BatchEffect batchelor
13 months ago José • 0
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6
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1.4k
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[DESeq2] Introduce a bias in DESeq2
DifferentialExpression DESeq2 BatchEffect
updated 13 months ago by 43k • written 14 months ago by • 0
5
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4
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1.0k
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How to control batch effect if Group and batch are same?
limma DESeq2 BatchEffect
updated 14 months ago by ★ 5.0k • written 14 months ago by • 0
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6
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1.5k
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heatmap with batch effect
DESeq2 BatchEffect
written 14 months ago by • 0
2
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2
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751
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Batch adjustment for cohort based RNA seq data
RNASeqPower removeBatchEffect cpm Batcheffect
14 months ago sukeshinik5 ▴ 20
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2
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724
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ReactomeGSA adjustment for confounding variables
BiologicalQuestion ReactomeGSA BatchEffect
written 15 months ago by • 0
4
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7
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2.2k
views
What does evidence of batch effect in bulk rnaseq look like?
surrogatevariables DESeq2 BatchEffect bulkrna-seq sva-seq
updated 16 months ago by ▴ 10 • written 17 months ago by ▴ 70
2
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2
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890
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Control group between 2 batches have different expression in RNAseq data
BatchQC BatchEffect rnaseqGene Normalization
updated 18 months ago by ▴ 10 • written 18 months ago by • 0
2
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2
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1.0k
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How to remove batch effect to combine RNAseq data from 2 different experiments?
BatchQC BatchEffect RNASeq
updated 18 months ago by ▴ 10 • written 18 months ago by • 0
0
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1
reply
730
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ReactomeGSA for RNASeq
ReactomeGSA BatchEffect RNASeqData
updated 15 months ago by ▴ 20 • written 18 months ago by • 0
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2
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2.1k
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Batch effect correction: methylome data
sesame BatchEffect MethylationArray
updated 19 months ago by ▴ 20 • written 19 months ago by • 0
2
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9
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1.8k
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Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2 RUVSeq RUVseq BatchEffect DES
updated 19 months ago by 68k • written 19 months ago by • 0
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2
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1.2k
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RNAseq:Technical replicates from different batches
technicalReplicates BatchEffect limma RNASeq
19 months ago catv • 0
0
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8
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1.6k
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DESeq and SVA for batch effect
DESeq2 BatchEffect sva
21 months ago michelafrancesconi8 • 0
1
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3
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1.1k
views
DESEQ2 Batch Effect
DESeq2 BatchEffect RNASeq
updated 21 months ago by ★ 1.4k • written 21 months ago by ▴ 10
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0
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589
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Can I combine collinear variables into a single value
BatchEffect limma
21 months ago Harrsha • 0
2
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1
reply
750
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Limma Question
DESeq2 BatchEffect limma RNASeq
updated 21 months ago by 43k • written 21 months ago by ▴ 10
4
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1
reply
1.9k
views
When should I correct for batch effects
BatchEffect SingleCellExperiment
updated 22 months ago by 68k • written 22 months ago by ▴ 20
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5
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1.9k
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Can SVs identified from sva be used for removeBatchEffect() in DESeq2
sva DESeq2 BatchEffect limma
updated 23 months ago by ★ 5.0k • written 23 months ago by • 0
2
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4
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1.8k
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Correct the batch effect in methylation analysis in R
BatchEffect limma methylationArrayAnalysis
updated 24 months ago by 53k • written 24 months ago by • 0
1
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4
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1.5k
views
controling for batch effect while preserving variation within repeated measures that unevenly distributed across batches
miRNA BatchEffect RNASeq limma
2.1 years ago Wending • 0
0
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4
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1.4k
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How to correct for known and surrogate variables in DESeq2?
DESeq2 BatchEffect sva limma
updated 19 months ago by 43k • written 2.1 years ago by • 0
0
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1
reply
860
views
Batch effect adjust in model matrix
BatchEffect edgeR
updated 2.2 years ago by ★ 5.0k • written 2.2 years ago by • 0
3
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5
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2.2k
views
Getting batch corrected counts after RUVSeq
BatchEffect RUVSeq RNASeq DESeq2
updated 2.2 years ago by ★ 5.0k • written 2.2 years ago by • 0
2
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5
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2.8k
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removing the batch effect for vst counts and defining the batches in removeBatchEffect function
DESeq2 BatchEffect limma
updated 2.3 years ago by 53k • written 2.3 years ago by • 0
2
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3
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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 2.3 years ago by 68k • written 2.3 years ago by ▴ 10
3
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4
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2.0k
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lfcShrink() and batch effects in DESeq2
BatchEffect lfcshrink RNA-seq DESeq2
2.3 years ago Eva ▴ 10
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2
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1.2k
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smallRNA-seq analysis batch correction in limma
BatchEffect limma
2.4 years ago Eleonora • 0
1
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1
reply
820
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Best way to handle batch effects from difference Mice?
RNASeqData BatchEffect edgeR limma
updated 2.4 years ago by 53k • written 2.4 years ago by • 0
2
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3
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2.5k
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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 2.4 years ago by ★ 5.0k • written 2.4 years ago by ▴ 10
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0
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878
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How to go for Batch correction in RNA-seq expeiment conducted based on imbalanced Experimental design ?
RNASeqData BatchEffect sva
2.4 years ago amnahsiddiqa ▴ 10
1
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1
reply
951
views
WGCNA Cluster batch effect
BatchEffect TCGA WGCNA
updated 2.4 years ago by ★ 5.0k • written 2.4 years ago by • 0
2
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5
replies
2.3k
views
DESeq2 remove batch effect
BatchEffect RNASeqData WGCNA DESeq2
updated 19 months ago by • 0 • written 2.5 years ago by • 0
1
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2
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1.8k
views
Batch effect between biological replicates
BatchEffect DESeq2
2.6 years ago gtechbio ▴ 10
0
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4
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1.8k
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Combine RNA-seq
BatchEffect R rnaseq
updated 2.6 years ago by ★ 1.4k • written 2.6 years ago by • 0
2
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4
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2.6k
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How to get TPM / FPKM after batch correction with DESeq2?
DESeq2 BatchEffect tpm fpkm
2.6 years ago vk • 0
2
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2
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1.8k
views
Error in checkFullRank(modelMatrix)
DESeq2 BatchEffect DifferentialExpression
updated 2.6 years ago by ★ 5.0k • written 2.6 years ago by ▴ 30
2
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3
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1.8k
views
Batch correction and Deseq2
DESeq2 WGCNA Normalization NormalyzerDE BatchEffect
updated 2.7 years ago by ★ 5.0k • written 2.7 years ago by ▴ 20
2
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1
reply
1.5k
views
How to identify the batch informations from the sample ID?
TCGAbiolinks BatchQC BatchEffect
updated 2.3 years ago by • 0 • written 2.7 years ago by ▴ 200
3
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2
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1.5k
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Batch question Bulk RNA-Seq
BatchEffect RNASeq
2.8 years ago • updated 2.7 years ago chf • 0
2
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1
reply
3.2k
views
DESeq2 design after combatseq batch correction
DESeq2 BatchEffect
updated 2.8 years ago by ★ 5.0k • written 2.8 years ago by • 0
0
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1
reply
810
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Analysis with Batch correction
DESeq2 BatchEffect
updated 2.8 years ago by 43k • written 2.8 years ago by • 0
1
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1
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1.3k
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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 2.8 years ago by 68k • written 2.8 years ago by • 0
5
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2
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1.4k
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Sva and batch effect
limma BatchEffect sva
updated 2.8 years ago by 53k • written 2.8 years ago by • 0
1
vote
1
reply
4.8k
views
batch effect correction before DESeq2 analysis
DESeq2 BatchEffect
updated 2.8 years ago by ★ 5.0k • written 2.9 years ago by ▴ 50
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0
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1.4k
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Trying to use a NanoString expression set with batch effects to do GSVA
GSVA Normalization BatchEffect GSVAdata NanoString
2.9 years ago Zhijie • 0
93 results • Page 1 of 2
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Replies
Comment: BiocParallel (and DESeq2) - wrong args for environment subassignment by Michael Love 43k
BTW, I tested with no issue on MacOS ARM on our previous github issue.
Answer: DESeq(dds, parallel=TRUE) wrong args for environment subassignment by Michael Love 43k
The DESeq2 error makes sense, as we've talked about, given that the simple `bplapply` isn't working in your setup. Maybe give the traceb…
Answer: PTM analysis in LIMPA by Gordon Smyth 53k
For PTM analysis, the usual quantification command dpcQuant() is replaced by dpcImpute(). Otherwise the limpa pipeline is the same as for a…
Answer: problem reading bam files into nucleR by James W. MacDonald 68k
The first step is to update to the current versions of R/Bioconductor and try again. It's possible that you have run into a bug that's alre…
Answer: Question about DESeq2 Design for Paired Treatment Study by ATpoint ★ 5.0k
It's a paired analysis so you don't need any patient-specific covariates such as age and sex. What you call batch effect might just be the …
Votes
C: DESeq2 Following RSEM
Upcoming Ensembl API and data access changes - new blog post available
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
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