Showing : batcheffect • reset
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How to remove batch effect to combine RNAseq data from 2 different experiments?
BatchQC BatchEffect RNASeq
updated 10 days ago by 66k • written 10 days ago by • 0
1
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1
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118
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Control group between 2 batches have different expression in RNAseq data
BatchQC BatchEffect rnaseqGene Normalization
updated 10 days ago by 66k • written 10 days ago by • 0
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0
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89
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ReactomeGSA for RNASeq
ReactomeGSA BatchEffect RNASeqData
14 days ago Shaimaa Gamal • 0
0
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2
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202
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Batch effect correction: methylome data
sesame BatchEffect MethylationArray
updated 16 days ago by ▴ 10 • written 18 days ago by • 0
2
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9
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465
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Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2 RUVSeq RUVseq BatchEffect DES
updated 5 weeks ago by 66k • written 5 weeks ago by • 0
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2
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263
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RNAseq:Technical replicates from different batches
technicalReplicates BatchEffect limma RNASeq
5 weeks ago catv • 0
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8
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475
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DESeq and SVA for batch effect
DESeq2 BatchEffect sva
12 weeks ago michelafrancesconi8 • 0
1
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3
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402
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DESEQ2 Batch Effect
DESeq2 BatchEffect RNASeq
updated 12 weeks ago by ★ 1.4k • written 12 weeks ago by ▴ 10
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0
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172
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Can I combine collinear variables into a single value
BatchEffect limma
3 months ago Harrsha • 0
2
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1
reply
286
views
Limma Question
DESeq2 BatchEffect limma RNASeq
updated 3 months ago by 42k • written 3 months ago by ▴ 10
4
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1
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406
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When should I correct for batch effects
BatchEffect SingleCellExperiment
updated 4 months ago by 66k • written 4 months ago by ▴ 20
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5
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634
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Can SVs identified from sva be used for removeBatchEffect() in DESeq2
sva DESeq2 BatchEffect limma
updated 4 months ago by ★ 4.2k • written 4 months ago by • 0
2
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4
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710
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Correct the batch effect in methylation analysis in R
BatchEffect limma methylationArrayAnalysis
updated 5 months ago by 50k • written 5 months ago by • 0
1
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4
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672
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controling for batch effect while preserving variation within repeated measures that unevenly distributed across batches
miRNA BatchEffect RNASeq limma
7 months ago • updated 6 months ago Wending • 0
0
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4
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651
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How to correct for known and surrogate variables in DESeq2?
DESeq2 BatchEffect sva limma
updated 6 weeks ago by 42k • written 7 months ago by • 0
0
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1
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483
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Batch effect adjust in model matrix
BatchEffect edgeR
updated 8 months ago by ★ 4.2k • written 8 months ago by • 0
3
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5
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920
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Getting batch corrected counts after RUVSeq
BatchEffect RUVSeq RNASeq DESeq2
updated 8 months ago by ★ 4.2k • written 8 months ago by • 0
2
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5
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1.4k
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removing the batch effect for vst counts and defining the batches in removeBatchEffect function
DESeq2 BatchEffect limma
updated 9 months ago by 50k • written 9 months ago by • 0
2
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3
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1.2k
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 9 months ago by 66k • written 9 months ago by ▴ 10
3
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4
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907
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lfcShrink() and batch effects in DESeq2
BatchEffect lfcshrink RNA-seq DESeq2
9 months ago Eva ▴ 10
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2
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660
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smallRNA-seq analysis batch correction in limma
BatchEffect limma
10 months ago Eleonora • 0
1
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1
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476
views
Best way to handle batch effects from difference Mice?
RNASeqData BatchEffect edgeR limma
updated 10 months ago by 50k • written 10 months ago by • 0
2
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3
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1.2k
views
PCA for QC should include subset of top variable genes or full set of genes in RNAseq data?
BatchQC RNASeqData sva BatchEffect
updated 11 months ago by ★ 4.2k • written 11 months ago by ▴ 10
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0
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415
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How to go for Batch correction in RNA-seq expeiment conducted based on imbalanced Experimental design ?
RNASeqData BatchEffect sva
11 months ago amnahsiddiqa ▴ 10
1
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1
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514
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WGCNA Cluster batch effect
BatchEffect TCGA WGCNA
updated 11 months ago by ★ 4.2k • written 11 months ago by • 0
2
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5
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1.2k
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DESeq2 remove batch effect
BatchEffect RNASeqData WGCNA DESeq2
updated 6 weeks ago by • 0 • written 11 months ago by • 0
1
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2
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1.0k
views
Batch effect between biological replicates
BatchEffect DESeq2
12 months ago gtechbio ▴ 10
0
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4
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940
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Combine RNA-seq
BatchEffect R rnaseq
updated 13 months ago by ★ 1.4k • written 13 months ago by • 0
2
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4
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1.5k
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How to get TPM / FPKM after batch correction with DESeq2?
DESeq2 BatchEffect tpm fpkm
13 months ago vk • 0
2
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2
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935
views
Error in checkFullRank(modelMatrix)
DESeq2 BatchEffect DifferentialExpression
updated 13 months ago by ★ 4.2k • written 13 months ago by ▴ 30
2
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3
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950
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Batch correction and Deseq2
DESeq2 WGCNA Normalization NormalyzerDE BatchEffect
updated 14 months ago by ★ 4.2k • written 14 months ago by ▴ 20
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1
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643
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How to identify the batch informations from the sample ID?
TCGAbiolinks BatchQC BatchEffect
updated 9 months ago by • 0 • written 14 months ago by ▴ 20
3
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2
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785
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Batch question Bulk RNA-Seq
BatchEffect RNASeq
14 months ago chf • 0
2
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1
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1.5k
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DESeq2 design after combatseq batch correction
DESeq2 BatchEffect
updated 15 months ago by ★ 4.2k • written 15 months ago by • 0
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1
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499
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Analysis with Batch correction
DESeq2 BatchEffect
updated 15 months ago by 42k • written 15 months ago by • 0
1
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1
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789
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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 15 months ago by 66k • written 15 months ago by • 0
5
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2
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802
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Sva and batch effect
limma BatchEffect sva
updated 16 months ago by 50k • written 16 months ago by • 0
1
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1
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1.8k
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batch effect correction before DESeq2 analysis
DESeq2 BatchEffect
updated 16 months ago by ★ 4.2k • written 16 months ago by ▴ 50
0
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0
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767
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Trying to use a NanoString expression set with batch effects to do GSVA
GSVA Normalization BatchEffect GSVAdata NanoString
17 months ago Zhijie • 0
1
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0
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705
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Use scran's normalization by deconvolution for each individual sample or over all samples
scran Normalization scRNA BatchEffect
17 months ago r_grau ▴ 10
1
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2
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924
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Design formula with batch effects DESeq2 "Not full rank matrix" error.
DESeq2 BatchEffect RNASeq
updated 19 months ago by ★ 1.4k • written 19 months ago by • 0
3
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10
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2.0k
views
Fold Change calculation when Batch Effect is present in RNA-seq data (DEseq2)
DESeq2 BatchEffect fold
20 months ago • updated 19 months ago eve.olszanowski • 0
1
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2
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813
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Modelling batch effect in DESeq2 - how to interpret the results?
DESeq2 BatchEffect
20 months ago annamariabugaj ▴ 10
0
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1
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1.0k
views
Batch effects in DESeq2: determination and model building
BatchEffect batch RNASeqR formula DESeq2
updated 21 months ago by 42k • written 21 months ago by • 0
0
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1
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899
views
Building model matrix to correct for batch effect with biological and technical replicates: Problem with linear correlations
MassSpectrometryData BatchEffect r limma
updated 22 months ago by 50k • written 22 months ago by • 0
1
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1
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722
views
RNA-Seq normalization and batch effect removal
RNASeq BatchEffect DESeq2
updated 24 months ago by 42k • written 24 months ago by • 0
6
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7
replies
1.9k
views
Batch effect with one sample being in two batches
BatchEffect DESeq2
24 months ago • updated 23 months ago lmrogers34 ▴ 10
2
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1
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1.3k
views
removeBatchEffect: Coefficients not estimable when using "batch matrix" for `covariates` argument.
limma BatchEffect
updated 24 months ago by 50k • written 24 months ago by ▴ 40
0
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1
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973
views
Differential methilation analysis batch effect removal
BatchEffect combat sva edgeR RRBSdata
updated 2.1 years ago by 50k • written 2.1 years ago by • 0
1
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1
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1.2k
views
How to determine if limma can adjust for batch effect
BatchEffect limma sva DifferentialExpression
updated 2.3 years ago by ★ 4.2k • written 2.3 years ago by ▴ 40
50 results • Page 1 of 1
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Comment: Deseq2 by Ram ▴ 210
Cross-posted on biostars: https://www.biostars.org/p/9596031/
Comment: SpliceWiz collateData error by giulia.nicoletto.1 • 0
Hi there, I am facing a similar error. When I try the collateData command collateData( Experiment = expr, reference_path = "./Referen…
Answer: Best way to describe DEseq2 design by SamGG ▴ 350
Hi, My own opinion. In the design `~ Batch`, ChemicalA_t1 is the intercept. So, all coefficients refer to this level as a reference. …
Answer: Deseq2 by ATpoint ★ 4.2k
Ser the vignette https://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html It covers prefiltering (and everyt…
Comment: Counter-directional LFC shrinkage by Michael Love 42k
Gene 1 is hard to predict given the paucity of data for the comparison of interest. What is happening is that the relatively low dispersion…
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Answer: Deseq2
Answer: limma Intercept vs No-intercept models completely changing DMR results?
Answer: limma Intercept vs No-intercept models completely changing DMR results?
Answer: When should I correct for batch effects
Answer: When should I correct for batch effects
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