Showing : BatchEffect • reset
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Batch correction for microarray
BatchEffect sva MicroarrayData
9 months ago Shaimaa Gamal • 0
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5
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798
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Is there a way to do DEG analysis across two batches sharing one sample only?
DESeq2 DifferentialExpression RNASeqData BatchEffect
written 12 months ago by • 0
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9
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1.9k
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Why did PCA plots look exactly the same after adjusting for batch covariate in DESeq2 design?
DESeq2 BatchEffect
12 months ago Quang NN ▴ 10
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4
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2.7k
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Differential Expression Analysis with unbalanced batches without replication between conditions
edgeR BatchEffect
updated 14 months ago by 53k • written 14 months ago by • 0
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2
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1.3k
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Integration of Single Cell Experiments with batchelor::fastMNN
fastMNN SingleCellData BatchEffect batchelor
15 months ago José • 0
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6
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1.5k
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[DESeq2] Introduce a bias in DESeq2
DifferentialExpression DESeq2 BatchEffect
updated 15 months ago by 43k • written 15 months ago by • 0
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4
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How to control batch effect if Group and batch are same?
limma DESeq2 BatchEffect
updated 15 months ago by ★ 5.0k • written 15 months ago by • 0
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6
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1.6k
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heatmap with batch effect
DESeq2 BatchEffect
written 15 months ago by • 0
2
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2
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813
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Batch adjustment for cohort based RNA seq data
RNASeqPower removeBatchEffect cpm Batcheffect
16 months ago sukeshinik5 ▴ 20
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2
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758
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ReactomeGSA adjustment for confounding variables
BiologicalQuestion ReactomeGSA BatchEffect
written 16 months ago by • 0
4
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7
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2.5k
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What does evidence of batch effect in bulk rnaseq look like?
surrogatevariables DESeq2 BatchEffect bulkrna-seq sva-seq
updated 17 months ago by ▴ 10 • written 18 months ago by ▴ 70
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948
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Control group between 2 batches have different expression in RNAseq data
BatchQC BatchEffect rnaseqGene Normalization
updated 19 months ago by ▴ 10 • written 20 months ago by • 0
2
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2
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1.1k
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How to remove batch effect to combine RNAseq data from 2 different experiments?
BatchQC BatchEffect RNASeq
updated 19 months ago by ▴ 10 • written 20 months ago by • 0
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1
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782
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ReactomeGSA for RNASeq
ReactomeGSA BatchEffect RNASeqData
updated 16 months ago by ▴ 20 • written 20 months ago by • 0
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2
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2.4k
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Batch effect correction: methylome data
sesame BatchEffect MethylationArray
updated 20 months ago by ▴ 20 • written 20 months ago by • 0
2
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9
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1.9k
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Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2 RUVSeq RUVseq BatchEffect DES
updated 21 months ago by 68k • written 21 months ago by • 0
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2
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1.4k
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RNAseq:Technical replicates from different batches
technicalReplicates BatchEffect limma RNASeq
21 months ago catv • 0
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8
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1.7k
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DESeq and SVA for batch effect
DESeq2 BatchEffect sva
22 months ago michelafrancesconi8 • 0
1
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3
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1.2k
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DESEQ2 Batch Effect
DESeq2 BatchEffect RNASeq
updated 22 months ago by ★ 1.4k • written 23 months ago by ▴ 10
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615
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Can I combine collinear variables into a single value
BatchEffect limma
23 months ago Harrsha • 0
2
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1
reply
797
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Limma Question
DESeq2 BatchEffect limma RNASeq
updated 23 months ago by 43k • written 23 months ago by ▴ 10
4
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1
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2.0k
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When should I correct for batch effects
BatchEffect SingleCellExperiment
updated 24 months ago by 68k • written 24 months ago by ▴ 20
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5
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2.1k
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Can SVs identified from sva be used for removeBatchEffect() in DESeq2
sva DESeq2 BatchEffect limma
updated 2.0 years ago by ★ 5.0k • written 2.0 years ago by • 0
2
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4
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1.9k
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Correct the batch effect in methylation analysis in R
BatchEffect limma methylationArrayAnalysis
updated 2.1 years ago by 53k • written 2.1 years ago by • 0
1
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4
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1.6k
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controling for batch effect while preserving variation within repeated measures that unevenly distributed across batches
miRNA BatchEffect RNASeq limma
2.2 years ago Wending • 0
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4
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1.5k
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How to correct for known and surrogate variables in DESeq2?
DESeq2 BatchEffect sva limma
updated 21 months ago by 43k • written 2.2 years ago by • 0
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1
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894
views
Batch effect adjust in model matrix
BatchEffect edgeR
updated 2.3 years ago by ★ 5.0k • written 2.3 years ago by • 0
3
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5
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2.3k
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Getting batch corrected counts after RUVSeq
BatchEffect RUVSeq RNASeq DESeq2
updated 2.4 years ago by ★ 5.0k • written 2.4 years ago by • 0
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5
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3.0k
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removing the batch effect for vst counts and defining the batches in removeBatchEffect function
DESeq2 BatchEffect 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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3.2k
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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 2.5 years ago by 68k • written 2.5 years ago by ▴ 10
3
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4
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2.3k
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lfcShrink() and batch effects in DESeq2
BatchEffect lfcshrink RNA-seq DESeq2
2.5 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
2.5 years ago Eleonora • 0
1
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1
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855
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Best way to handle batch effects from difference Mice?
RNASeqData BatchEffect edgeR limma
updated 2.5 years ago by 53k • written 2.5 years ago by • 0
2
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3
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2.7k
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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 2.6 years ago by ★ 5.0k • written 2.6 years ago by ▴ 10
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0
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917
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How to go for Batch correction in RNA-seq expeiment conducted based on imbalanced Experimental design ?
RNASeqData BatchEffect sva
2.6 years ago amnahsiddiqa ▴ 10
1
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1
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986
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WGCNA Cluster batch effect
BatchEffect TCGA WGCNA
updated 2.6 years ago by ★ 5.0k • written 2.6 years ago by • 0
2
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5
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2.4k
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DESeq2 remove batch effect
BatchEffect RNASeqData WGCNA DESeq2
updated 21 months ago by • 0 • written 2.6 years ago by • 0
1
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2
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1.9k
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Batch effect between biological replicates
BatchEffect DESeq2
2.7 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 2.7 years ago by ★ 1.4k • written 2.7 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
2.8 years ago vk • 0
2
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2
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1.9k
views
Error in checkFullRank(modelMatrix)
DESeq2 BatchEffect DifferentialExpression
updated 2.8 years ago by ★ 5.0k • written 2.8 years ago by ▴ 20
2
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3
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1.9k
views
Batch correction and Deseq2
DESeq2 WGCNA Normalization NormalyzerDE BatchEffect
updated 2.8 years ago by ★ 5.0k • written 2.9 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 2.4 years ago by • 0 • written 2.9 years ago by ▴ 200
3
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2
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1.6k
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Batch question Bulk RNA-Seq
BatchEffect RNASeq
2.9 years ago chf • 0
2
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1
reply
3.3k
views
DESeq2 design after combatseq batch correction
DESeq2 BatchEffect
updated 2.9 years ago by ★ 5.0k • written 2.9 years ago by • 0
0
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1
reply
842
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Analysis with Batch correction
DESeq2 BatchEffect
updated 2.9 years ago by 43k • written 2.9 years ago by • 0
1
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1
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1.4k
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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 2.9 years ago by 68k • written 2.9 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 3.0 years ago by 53k • written 3.0 years ago by • 0
1
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1
reply
5.0k
views
batch effect correction before DESeq2 analysis
DESeq2 BatchEffect
updated 3.0 years ago by ★ 5.0k • written 3.0 years ago by ▴ 50
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0
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1.5k
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Trying to use a NanoString expression set with batch effects to do GSVA
GSVA Normalization BatchEffect GSVAdata NanoString
3.0 years ago Zhijie • 0
93 results • Page 1 of 2
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Comment: Combining two proteomics datasets with limpa by Andrew Pattison • 0
Thanks heaps Gordon. I went with option 1 and no normalisation and all seems to have worked well. Cheers, Andrew
Comment: limpa-blank normalization and Spectronaut's PTM stoichiometry by Gordon Smyth 53k
Flagging protein groups as likely contaminants in this way will be fine for a limpa analysis. The `Cont_` proteins can optionally stay in f…
Answer: Making a Full Rank Model for Allele-Specific Expression with DESeq2 by Gordon Smyth 53k
I think that some historical context will help here. Aaron Lun was a PhD student in my Lab back in 2015, and the analysis approach that he …
Comment: Making a Full Rank Model for Allele-Specific Expression with DESeq2 by Michael Love 43k
You just need the mouse identifier (controls baseline) and the group specific allelic effect.
Comment: limpa-blank normalization and Spectronaut's PTM stoichiometry by Julia Broadbent • 0
Hi Emily, Just sharing a resource for handling contaminants - we use the methods described in [Frankenfield et al. (2022)](https://pubs.acs…
Votes
A: Filtering read counts matrix: how to deal with duplicated gene symbols, differen
Comment: limpa analysis advice
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
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