Showing : Batcheffect • reset
0
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5
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Is there a way to do DEG analysis across two batches sharing one sample only?
DESeq2 DifferentialExpression RNASeqData BatchEffect
written 6 weeks ago by • 0
2
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9
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977
views
Why did PCA plots look exactly the same after adjusting for batch covariate in DESeq2 design?
DESeq2 BatchEffect
8 weeks ago • updated 6 weeks ago Quang NN ▴ 10
2
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4
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1.8k
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Differential Expression Analysis with unbalanced batches without replication between conditions
edgeR BatchEffect
updated 3 months ago by 52k • written 3 months ago by • 0
0
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2
replies
701
views
Integration of Single Cell Experiments with batchelor::fastMNN
fastMNN SingleCellData BatchEffect batchelor
4 months ago José • 0
0
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6
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978
views
[DESeq2] Introduce a bias in DESeq2
DifferentialExpression DESeq2 BatchEffect
updated 4 months ago by 43k • written 4 months ago by • 0
5
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4
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618
views
How to control batch effect if Group and batch are same?
limma DESeq2 BatchEffect
updated 4 months ago by ★ 4.7k • written 5 months ago by • 0
0
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5
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834
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heatmap with batch effect
DESeq2 BatchEffect
5 months ago tothuhien • 0
2
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2
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451
views
Batch adjustment for cohort based RNA seq data
RNASeqPower removeBatchEffect cpm Batcheffect
5 months ago sukeshinik5 ▴ 20
0
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2
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469
views
ReactomeGSA adjustment for confounding variables
BiologicalQuestion ReactomeGSA BatchEffect
written 6 months ago by • 0
4
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7
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1.5k
views
What does evidence of batch effect in bulk rnaseq look like?
surrogatevariables DESeq2 BatchEffect bulkrna-seq sva-seq
updated 7 months ago by ▴ 10 • written 8 months ago by ▴ 70
2
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2
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639
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Control group between 2 batches have different expression in RNAseq data
BatchQC BatchEffect rnaseqGene Normalization
updated 9 months ago by ▴ 10 • written 9 months ago by • 0
2
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2
replies
738
views
How to remove batch effect to combine RNAseq data from 2 different experiments?
BatchQC BatchEffect RNASeq
updated 9 months ago by ▴ 10 • written 9 months ago by • 0
0
votes
1
reply
447
views
ReactomeGSA for RNASeq
ReactomeGSA BatchEffect RNASeqData
updated 6 months ago by ▴ 20 • written 9 months ago by • 0
0
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2
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1.3k
views
Batch effect correction: methylome data
sesame BatchEffect MethylationArray
updated 9 months ago by ▴ 20 • written 9 months ago by • 0
2
votes
9
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1.2k
views
Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2 RUVSeq RUVseq BatchEffect DES
updated 10 months ago by 68k • written 10 months ago by • 0
0
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2
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758
views
RNAseq:Technical replicates from different batches
technicalReplicates BatchEffect limma RNASeq
10 months ago catv • 0
0
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8
replies
1.0k
views
DESeq and SVA for batch effect
DESeq2 BatchEffect sva
12 months ago michelafrancesconi8 • 0
1
vote
3
replies
808
views
DESEQ2 Batch Effect
DESeq2 BatchEffect RNASeq
updated 12 months ago by ★ 1.4k • written 12 months ago by ▴ 10
0
votes
0
replies
433
views
Can I combine collinear variables into a single value
BatchEffect limma
12 months ago Harrsha • 0
2
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1
reply
561
views
Limma Question
DESeq2 BatchEffect limma RNASeq
updated 12 months ago by 43k • written 12 months ago by ▴ 10
4
votes
1
reply
1.3k
views
When should I correct for batch effects
BatchEffect SingleCellExperiment
updated 13 months ago by 68k • written 13 months ago by ▴ 20
0
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5
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1.5k
views
Can SVs identified from sva be used for removeBatchEffect() in DESeq2
sva DESeq2 BatchEffect limma
updated 14 months ago by ★ 4.7k • written 14 months ago by • 0
2
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4
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1.4k
views
Correct the batch effect in methylation analysis in R
BatchEffect limma methylationArrayAnalysis
updated 15 months ago by 52k • written 15 months ago by • 0
1
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4
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1.1k
views
controling for batch effect while preserving variation within repeated measures that unevenly distributed across batches
miRNA BatchEffect RNASeq limma
16 months ago Wending • 0
0
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4
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1.1k
views
How to correct for known and surrogate variables in DESeq2?
DESeq2 BatchEffect sva limma
updated 10 months ago by 43k • written 16 months ago by • 0
0
votes
1
reply
711
views
Batch effect adjust in model matrix
BatchEffect edgeR
updated 17 months ago by ★ 4.7k • written 17 months ago by • 0
3
votes
5
replies
1.7k
views
Getting batch corrected counts after RUVSeq
BatchEffect RUVSeq RNASeq DESeq2
updated 18 months ago by ★ 4.7k • written 18 months ago by • 0
2
votes
5
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2.3k
views
removing the batch effect for vst counts and defining the batches in removeBatchEffect function
DESeq2 BatchEffect limma
updated 19 months ago by 52k • written 19 months ago by • 0
2
votes
3
replies
2.3k
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 19 months ago by 68k • written 19 months ago by ▴ 10
3
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4
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1.5k
views
lfcShrink() and batch effects in DESeq2
BatchEffect lfcshrink RNA-seq DESeq2
19 months ago Eva ▴ 10
0
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2
replies
962
views
smallRNA-seq analysis batch correction in limma
BatchEffect limma
19 months ago Eleonora • 0
1
vote
1
reply
684
views
Best way to handle batch effects from difference Mice?
RNASeqData BatchEffect edgeR limma
updated 20 months ago by 52k • written 20 months ago by • 0
2
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3
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2.1k
views
PCA for QC should include subset of top variable genes or full set of genes in RNAseq data?
BatchQC RNASeqData sva BatchEffect
updated 20 months ago by ★ 4.7k • written 20 months ago by ▴ 10
0
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0
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648
views
How to go for Batch correction in RNA-seq expeiment conducted based on imbalanced Experimental design ?
RNASeqData BatchEffect sva
20 months ago amnahsiddiqa ▴ 10
1
vote
1
reply
754
views
WGCNA Cluster batch effect
BatchEffect TCGA WGCNA
updated 20 months ago by ★ 4.7k • written 20 months ago by • 0
2
votes
5
replies
1.9k
views
DESeq2 remove batch effect
BatchEffect RNASeqData WGCNA DESeq2
updated 10 months ago by • 0 • written 21 months ago by • 0
1
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2
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1.5k
views
Batch effect between biological replicates
BatchEffect DESeq2
22 months ago • updated 21 months ago gtechbio ▴ 10
0
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4
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1.5k
views
Combine RNA-seq
BatchEffect R rnaseq
updated 22 months ago by ★ 1.4k • written 22 months ago by • 0
2
votes
4
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2.2k
views
How to get TPM / FPKM after batch correction with DESeq2?
DESeq2 BatchEffect tpm fpkm
23 months ago • updated 22 months ago vk • 0
2
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2
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1.4k
views
Error in checkFullRank(modelMatrix)
DESeq2 BatchEffect DifferentialExpression
updated 23 months ago by ★ 4.7k • written 23 months ago by ▴ 30
2
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3
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1.4k
views
Batch correction and Deseq2
DESeq2 WGCNA Normalization NormalyzerDE BatchEffect
updated 23 months ago by ★ 4.7k • written 24 months ago by ▴ 20
2
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1
reply
1.0k
views
How to identify the batch informations from the sample ID?
TCGAbiolinks BatchQC BatchEffect
updated 18 months ago by • 0 • written 24 months ago by ▴ 200
3
votes
2
replies
1.2k
views
Batch question Bulk RNA-Seq
BatchEffect RNASeq
24 months ago chf • 0
2
votes
1
reply
2.7k
views
DESeq2 design after combatseq batch correction
DESeq2 BatchEffect
updated 2.0 years ago by ★ 4.7k • written 2.0 years ago by • 0
0
votes
1
reply
671
views
Analysis with Batch correction
DESeq2 BatchEffect
updated 2.0 years ago by 43k • written 2.1 years ago by • 0
1
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1
reply
1.1k
views
Batch effect: Is it correct to put ~0 preparing the model.matrix to remove batch effect?
edgeR model.matrix BatchEffect
updated 2.1 years ago by 68k • written 2.1 years ago by • 0
5
votes
2
replies
1.1k
views
Sva and batch effect
limma BatchEffect sva
updated 2.1 years ago by 52k • written 2.1 years ago by • 0
1
vote
1
reply
3.8k
views
batch effect correction before DESeq2 analysis
DESeq2 BatchEffect
updated 2.1 years ago by ★ 4.7k • written 2.1 years ago by ▴ 50
0
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0
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1.2k
views
Trying to use a NanoString expression set with batch effects to do GSVA
GSVA Normalization BatchEffect GSVAdata NanoString
2.2 years ago Zhijie • 0
1
vote
0
replies
1.0k
views
Use scran's normalization by deconvolution for each individual sample or over all samples
scran Normalization scRNA BatchEffect
2.2 years ago r_grau ▴ 10
50 results • Page 1 of 1
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Answer: library org.Hs.eg.db failing to install by James W. MacDonald 68k
It should just install. ``` > library(BiocManager) Bioconductor version 3.20 (BiocManager 1.30.25), R 4.4.1 (2024-06-14 ucrt) W…
Comment: Surprising behavior for DEXseq dispersion estimate plot? by Elijah • 0
Thank you so much for your quick reply! I was worried if some underlying technical artifact or unusual behavior would be causing the patter…
Answer: Surprising behavior for DEXseq dispersion estimate plot? by Michael Love 43k
The red points are just slowly moving toward -Inf. They tend to have variance < mean (if it were a simple design and you could just look at…
Answer: DESeq use in lipidomic analysis by Michael Love 43k
I would go for limma rather than a NB-based method. See the papers on limma for metabolomics / proteomics.
Answer: DiffBind - question on the use of filtered or unfiltered input data by robert • 0
[FFH4X][1] Injector is a Free Fire mod menu software that includes a variety of intriguing hack features such as aimbot, auto headshot, fly…
Votes
Answer: Surprising behavior for DEXseq dispersion estimate plot?
Answer: Surprising behavior for DEXseq dispersion estimate plot?
Answer: Surprising behavior for DEXseq dispersion estimate plot?
Calculating TOM in blockwise WGCNA
A: What is the "linear model" part used for in Limma?
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