Showing : batcheffect • reset
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Batch correction for microarray
BatchEffect sva MicroarrayData
6 months ago Shaimaa Gamal • 0
0
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5
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669
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Is there a way to do DEG analysis across two batches sharing one sample only?
DESeq2 DifferentialExpression RNASeqData BatchEffect
written 9 months ago by • 0
2
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9
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1.6k
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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
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4
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2.4k
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Differential Expression Analysis with unbalanced batches without replication between conditions
edgeR BatchEffect
updated 11 months ago by 53k • written 11 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
12 months ago José • 0
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6
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1.3k
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[DESeq2] Introduce a bias in DESeq2
DifferentialExpression DESeq2 BatchEffect
updated 11 months ago by 43k • written 12 months ago by • 0
5
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4
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957
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How to control batch effect if Group and batch are same?
limma DESeq2 BatchEffect
updated 12 months ago by ★ 5.0k • written 12 months ago by • 0
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6
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1.4k
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heatmap with batch effect
DESeq2 BatchEffect
written 12 months ago by • 0
2
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2
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712
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Batch adjustment for cohort based RNA seq data
RNASeqPower removeBatchEffect cpm Batcheffect
13 months ago sukeshinik5 ▴ 20
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2
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681
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ReactomeGSA adjustment for confounding variables
BiologicalQuestion ReactomeGSA BatchEffect
written 13 months ago by • 0
4
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7
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2.1k
views
What does evidence of batch effect in bulk rnaseq look like?
surrogatevariables DESeq2 BatchEffect bulkrna-seq sva-seq
updated 14 months ago by ▴ 10 • written 15 months ago by ▴ 70
2
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2
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842
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Control group between 2 batches have different expression in RNAseq data
BatchQC BatchEffect rnaseqGene Normalization
updated 16 months ago by ▴ 10 • written 17 months ago by • 0
2
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2
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984
views
How to remove batch effect to combine RNAseq data from 2 different experiments?
BatchQC BatchEffect RNASeq
updated 16 months ago by ▴ 10 • written 17 months ago by • 0
0
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1
reply
660
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ReactomeGSA for RNASeq
ReactomeGSA BatchEffect RNASeqData
updated 13 months ago by ▴ 20 • written 17 months ago by • 0
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2
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2.0k
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Batch effect correction: methylome data
sesame BatchEffect MethylationArray
updated 17 months ago by ▴ 20 • written 17 months ago by • 0
2
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9
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1.7k
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Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2 RUVSeq RUVseq BatchEffect DES
updated 18 months ago by 68k • written 18 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
18 months ago catv • 0
0
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8
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1.4k
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DESeq and SVA for batch effect
DESeq2 BatchEffect sva
19 months ago michelafrancesconi8 • 0
1
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3
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1.0k
views
DESEQ2 Batch Effect
DESeq2 BatchEffect RNASeq
updated 19 months ago by ★ 1.4k • written 19 months ago by ▴ 10
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0
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567
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Can I combine collinear variables into a single value
BatchEffect limma
19 months ago Harrsha • 0
2
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1
reply
715
views
Limma Question
DESeq2 BatchEffect limma RNASeq
updated 20 months ago by 43k • written 20 months ago by ▴ 10
4
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1
reply
1.8k
views
When should I correct for batch effects
BatchEffect SingleCellExperiment
updated 21 months ago by 68k • written 21 months ago by ▴ 20
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5
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1.9k
views
Can SVs identified from sva be used for removeBatchEffect() in DESeq2
sva DESeq2 BatchEffect limma
updated 21 months ago by ★ 5.0k • written 21 months ago by • 0
2
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4
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1.7k
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Correct the batch effect in methylation analysis in R
BatchEffect limma methylationArrayAnalysis
updated 22 months ago by 53k • written 22 months ago by • 0
1
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4
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1.4k
views
controling for batch effect while preserving variation within repeated measures that unevenly distributed across batches
miRNA BatchEffect RNASeq limma
23 months 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 18 months ago by 43k • written 24 months ago by • 0
0
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1
reply
830
views
Batch effect adjust in model matrix
BatchEffect edgeR
updated 2.1 years ago by ★ 5.0k • written 2.1 years ago by • 0
3
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5
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2.1k
views
Getting batch corrected counts after RUVSeq
BatchEffect RUVSeq RNASeq DESeq2
updated 2.1 years ago by ★ 5.0k • written 2.1 years ago by • 0
2
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5
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2.7k
views
removing the batch effect for vst counts and defining the batches in removeBatchEffect function
DESeq2 BatchEffect limma
updated 2.2 years ago by 53k • written 2.2 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 2.2 years ago by 68k • written 2.2 years ago by ▴ 10
3
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4
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1.9k
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lfcShrink() and batch effects in DESeq2
BatchEffect lfcshrink RNA-seq DESeq2
2.2 years ago Eva ▴ 10
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2
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1.1k
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smallRNA-seq analysis batch correction in limma
BatchEffect limma
2.3 years ago Eleonora • 0
1
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1
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790
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Best way to handle batch effects from difference Mice?
RNASeqData BatchEffect edgeR 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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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 ★ 5.0k • written 2.3 years ago by ▴ 10
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0
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848
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
903
views
WGCNA Cluster batch effect
BatchEffect TCGA WGCNA
updated 2.3 years ago by ★ 5.0k • written 2.3 years ago by • 0
2
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5
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2.3k
views
DESeq2 remove batch effect
BatchEffect RNASeqData WGCNA DESeq2
updated 18 months ago by • 0 • written 2.4 years ago by • 0
1
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2
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1.8k
views
Batch effect between biological replicates
BatchEffect DESeq2
2.4 years ago gtechbio ▴ 10
0
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4
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1.7k
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Combine RNA-seq
BatchEffect R rnaseq
updated 2.5 years ago by ★ 1.4k • written 2.5 years ago by • 0
2
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4
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2.5k
views
How to get TPM / FPKM after batch correction with DESeq2?
DESeq2 BatchEffect tpm fpkm
2.5 years ago vk • 0
2
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2
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1.7k
views
Error in checkFullRank(modelMatrix)
DESeq2 BatchEffect DifferentialExpression
updated 2.5 years ago by ★ 5.0k • written 2.5 years ago by ▴ 30
2
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3
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1.7k
views
Batch correction and Deseq2
DESeq2 WGCNA Normalization NormalyzerDE BatchEffect
updated 2.6 years ago by ★ 5.0k • written 2.6 years ago by ▴ 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 • 0 • written 2.6 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
2.6 years ago chf • 0
2
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1
reply
3.2k
views
DESeq2 design after combatseq batch correction
DESeq2 BatchEffect
updated 2.7 years ago by ★ 5.0k • written 2.7 years ago by • 0
0
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1
reply
775
views
Analysis with Batch correction
DESeq2 BatchEffect
updated 2.7 years ago by 43k • written 2.7 years ago by • 0
1
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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 68k • written 2.7 years ago by • 0
5
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2
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1.3k
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Sva and batch effect
limma BatchEffect sva
updated 2.7 years ago by 53k • written 2.7 years ago by • 0
1
vote
1
reply
4.7k
views
batch effect correction before DESeq2 analysis
DESeq2 BatchEffect
updated 2.7 years ago by ★ 5.0k • written 2.7 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
2.8 years ago Zhijie • 0
93 results • Page 1 of 2
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Replies
Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in by dan.gatti • 0
I am, but perhaps I'm not understanding how it should work. > sse = DropletUtils::read10xCounts(curr_files[1], mtx.class = 'SVT_Sparse…
Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in by James W. MacDonald 68k
Did you use the development version as Aaron suggested? There is an argument to read the market matrix file directly into an `SVT_SparseMat…
Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in by dan.gatti • 0
Was anyone else able to put the pieces together using the reply above? I read in one 10X sample using DropletUtils::read10xCounts() and thi…
Comment: Announcing GBCC 2025: The first-ever joint conference between Bioconductor and G by dzv20413 • 0
Wow, GBCC 2025 sounds amazing, can not wait to see the logo contest results! Also, I just played [Level Devil][1] and it is super addictive…
Comment: Memory error while running alignments by Erik Wright ▴ 150
How much memory is available on the computer? A distance matrix of 50k sequences requires at least 50k*50k/2 * 8 bytes = 10GB, assuming the…
Votes
Comment: Check removeBatchEffect effectiveness
Comment: Streamlining the computing time for MiloDE p-value correction in large dataset?
Answer: DESeq2 design for haplotype MPRA
A: Different logFC (log2foldchange) values for genes from limma-voom and other too
Comment: Check removeBatchEffect effectiveness
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