Showing : batcheffect • reset
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Batch correction for microarray
BatchEffect sva MicroarrayData
10 months ago Shaimaa Gamal • 0
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5
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837
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Is there a way to do DEG analysis across two batches sharing one sample only?
DESeq2 DifferentialExpression RNASeqData BatchEffect
written 13 months ago by • 0
2
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9
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2.1k
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Why did PCA plots look exactly the same after adjusting for batch covariate in DESeq2 design?
DESeq2 BatchEffect
13 months ago Quang NN ▴ 10
2
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4
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2.9k
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Differential Expression Analysis with unbalanced batches without replication between conditions
edgeR BatchEffect
updated 15 months ago by 53k • written 15 months ago by • 0
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2
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1.7k
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Integration of Single Cell Experiments with batchelor::fastMNN
fastMNN SingleCellData BatchEffect batchelor
16 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 16 months ago by 43k • written 16 months ago by • 0
5
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4
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1.2k
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How to control batch effect if Group and batch are same?
limma DESeq2 BatchEffect
updated 16 months ago by ★ 5.0k • written 16 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 16 months ago by • 0
2
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2
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875
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Batch adjustment for cohort based RNA seq data
RNASeqPower removeBatchEffect cpm Batcheffect
17 months ago sukeshinik5 ▴ 20
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2
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782
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ReactomeGSA adjustment for confounding variables
BiologicalQuestion ReactomeGSA BatchEffect
written 17 months ago by • 0
4
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7
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2.8k
views
What does evidence of batch effect in bulk rnaseq look like?
surrogatevariables DESeq2 BatchEffect bulkrna-seq sva-seq
updated 18 months ago by ▴ 10 • written 20 months ago by ▴ 70
2
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2
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996
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Control group between 2 batches have different expression in RNAseq data
BatchQC BatchEffect rnaseqGene Normalization
updated 21 months ago by ▴ 10 • written 21 months ago by • 0
2
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2
replies
1.1k
views
How to remove batch effect to combine RNAseq data from 2 different experiments?
BatchQC BatchEffect RNASeq
updated 21 months ago by ▴ 10 • written 21 months ago by • 0
0
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1
reply
816
views
ReactomeGSA for RNASeq
ReactomeGSA BatchEffect RNASeqData
updated 17 months ago by ▴ 20 • written 21 months ago by • 0
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2
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2.6k
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Batch effect correction: methylome data
sesame BatchEffect MethylationArray
updated 21 months ago by ▴ 20 • written 21 months ago by • 0
2
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9
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2.0k
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Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2 RUVSeq RUVseq BatchEffect DES
updated 22 months ago by 68k • written 22 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
22 months ago catv • 0
0
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8
replies
1.7k
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DESeq and SVA for batch effect
DESeq2 BatchEffect sva
23 months ago michelafrancesconi8 • 0
1
vote
3
replies
1.2k
views
DESEQ2 Batch Effect
DESeq2 BatchEffect RNASeq
updated 24 months ago by ★ 1.4k • written 24 months ago by ▴ 10
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0
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630
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Can I combine collinear variables into a single value
BatchEffect limma
24 months ago Harrsha • 0
2
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1
reply
819
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Limma Question
DESeq2 BatchEffect limma RNASeq
updated 24 months ago by 43k • written 24 months ago by ▴ 10
4
votes
1
reply
2.1k
views
When should I correct for batch effects
BatchEffect SingleCellExperiment
updated 2.1 years ago by 68k • written 2.1 years ago by ▴ 20
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5
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2.1k
views
Can SVs identified from sva be used for removeBatchEffect() in DESeq2
sva DESeq2 BatchEffect limma
updated 2.1 years ago by ★ 5.0k • written 2.1 years ago by • 0
2
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4
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2.0k
views
Correct the batch effect in methylation analysis in R
BatchEffect limma methylationArrayAnalysis
updated 2.2 years ago by 53k • written 2.2 years ago by • 0
1
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4
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1.7k
views
controling for batch effect while preserving variation within repeated measures that unevenly distributed across batches
miRNA BatchEffect RNASeq limma
2.3 years ago Wending • 0
0
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4
replies
1.5k
views
How to correct for known and surrogate variables in DESeq2?
DESeq2 BatchEffect sva limma
updated 22 months ago by 43k • written 2.3 years ago by • 0
0
votes
1
reply
911
views
Batch effect adjust in model matrix
BatchEffect edgeR
updated 2.4 years ago by ★ 5.0k • written 2.4 years ago by • 0
3
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5
replies
2.4k
views
Getting batch corrected counts after RUVSeq
BatchEffect RUVSeq RNASeq DESeq2
updated 2.4 years ago by ★ 5.0k • written 2.5 years ago by • 0
2
votes
5
replies
3.2k
views
removing the batch effect for vst counts and defining the batches in removeBatchEffect function
DESeq2 BatchEffect limma
updated 2.5 years ago by 53k • written 2.5 years ago by • 0
2
votes
3
replies
3.3k
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 2.5 years ago by 68k • written 2.5 years ago by ▴ 10
3
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4
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2.5k
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lfcShrink() and batch effects in DESeq2
BatchEffect lfcshrink RNA-seq DESeq2
2.5 years ago Eva ▴ 30
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2
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1.3k
views
smallRNA-seq analysis batch correction in limma
BatchEffect limma
2.6 years ago Eleonora • 0
1
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1
reply
878
views
Best way to handle batch effects from difference Mice?
RNASeqData BatchEffect edgeR limma
updated 2.6 years ago by 53k • written 2.6 years ago by • 0
2
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3
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2.9k
views
PCA for QC should include subset of top variable genes or full set of genes in RNAseq data?
BatchQC RNASeqData sva BatchEffect
updated 2.7 years ago by ★ 5.0k • written 2.7 years ago by ▴ 10
0
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0
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934
views
How to go for Batch correction in RNA-seq expeiment conducted based on imbalanced Experimental design ?
RNASeqData BatchEffect sva
2.7 years ago amnahsiddiqa ▴ 10
1
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1
reply
1.0k
views
WGCNA Cluster batch effect
BatchEffect TCGA WGCNA
updated 2.7 years ago by ★ 5.0k • written 2.7 years ago by • 0
2
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5
replies
2.5k
views
DESeq2 remove batch effect
BatchEffect RNASeqData WGCNA DESeq2
updated 22 months ago by • 0 • written 2.7 years ago by • 0
1
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2
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1.9k
views
Batch effect between biological replicates
BatchEffect DESeq2
2.8 years ago gtechbio ▴ 10
0
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4
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1.9k
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Combine RNA-seq
BatchEffect R rnaseq
updated 2.8 years ago by ★ 1.4k • written 2.8 years ago by • 0
2
votes
4
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2.7k
views
How to get TPM / FPKM after batch correction with DESeq2?
DESeq2 BatchEffect tpm fpkm
2.9 years ago vk • 0
2
votes
2
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1.9k
views
Error in checkFullRank(modelMatrix)
DESeq2 BatchEffect DifferentialExpression
updated 2.9 years ago by ★ 5.0k • written 2.9 years ago by ▴ 20
2
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3
replies
2.0k
views
Batch correction and Deseq2
DESeq2 WGCNA Normalization NormalyzerDE BatchEffect
updated 2.9 years ago by ★ 5.0k • written 3.0 years ago by ▴ 20
2
votes
1
reply
1.6k
views
How to identify the batch informations from the sample ID?
TCGAbiolinks BatchQC BatchEffect
updated 2.5 years ago by • 0 • written 3.0 years ago by ▴ 200
3
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2
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1.6k
views
Batch question Bulk RNA-Seq
BatchEffect RNASeq
3.0 years ago chf • 0
2
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1
reply
3.5k
views
DESeq2 design after combatseq batch correction
DESeq2 BatchEffect
updated 3.0 years ago by ★ 5.0k • written 3.0 years ago by • 0
0
votes
1
reply
857
views
Analysis with Batch correction
DESeq2 BatchEffect
updated 3.0 years ago by 43k • written 3.0 years ago by • 0
1
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1
reply
1.4k
views
Batch effect: Is it correct to put ~0 preparing the model.matrix to remove batch effect?
edgeR model.matrix BatchEffect
updated 3.0 years ago by 68k • written 3.0 years ago by • 0
5
votes
2
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1.5k
views
Sva and batch effect
limma BatchEffect sva
updated 3.1 years ago by 53k • written 3.1 years ago by • 0
1
vote
1
reply
5.3k
views
batch effect correction before DESeq2 analysis
DESeq2 BatchEffect
updated 3.1 years ago by ★ 5.0k • written 3.1 years ago by ▴ 50
0
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0
replies
1.5k
views
Trying to use a NanoString expression set with batch effects to do GSVA
GSVA Normalization BatchEffect GSVAdata NanoString
3.1 years ago Zhijie • 0
93 results • Page 1 of 2
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Comment: Question on processing compound protein groups in limpa by JKim • 0
Many thanks. I appreciate your advice.
Answer: Question on processing compound protein groups in limpa by Gordon Smyth 53k
Different people have different ways of dealing with compound protein groups. You could just leave them in the analysis, in which case limp…
Answer: Correct usage of limpa for protein input by Gordon Smyth 53k
limpa can work on protein-level quantifications, but they must be intensity-based and must be on the log scale. From what I read (<https://…
Comment: A problem occurs when running the monocle2 by a2a2hset32aa • 0
Troubleshooting monocle2 errors in R 4.5.1 often points to package incompatibilities, particularly with newer versions of igraph. For resea…
Comment: Deadline Extended: EuroBioC2026 Call for Abstracts by a2a2hset32aa • 0
Attending EuroBioC2026 is an excellent way for researchers to explore the intersection of technology and biology. For those seeking high qu…
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Answer: Question on processing compound protein groups in limpa
Answer: Correct usage of limpa for protein input
Answer: Correct usage of limpa for protein input
Answer: Correct usage of limpa for protein input
A: Interpretaion of dendrogram height in WGCNA?
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