Showing : batcheffect • reset
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Is there a way to do DEG analysis across two batches sharing one sample only?
DESeq2 DifferentialExpression RNASeqData BatchEffect
3 hours ago • updated 2 hours ago georgeyu703 • 0
2
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9
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720
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Why did PCA plots look exactly the same after adjusting for batch covariate in DESeq2 design?
DESeq2 BatchEffect
13 days ago • updated 1 day ago QN ▴ 10
2
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4
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1.7k
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Differential Expression Analysis with unbalanced batches without replication between conditions
edgeR BatchEffect
updated 10 weeks ago by 52k • written 10 weeks ago by • 0
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2
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572
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Integration of Single Cell Experiments with batchelor::fastMNN
fastMNN SingleCellData BatchEffect batchelor
3 months ago José • 0
0
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6
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889
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[DESeq2] Introduce a bias in DESeq2
DifferentialExpression DESeq2 BatchEffect
updated 12 weeks ago by 43k • written 3 months ago by • 0
5
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4
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523
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How to control batch effect if Group and batch are same?
limma DESeq2 BatchEffect
updated 3 months ago by ★ 4.6k • written 3 months ago by • 0
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5
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703
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heatmap with batch effect
DESeq2 BatchEffect
3 months ago tothuhien • 0
2
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2
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379
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Batch adjustment for cohort based RNA seq data
RNASeqPower removeBatchEffect cpm Batcheffect
3 months ago sukeshinik5 ▴ 20
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2
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427
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ReactomeGSA adjustment for confounding variables
BiologicalQuestion ReactomeGSA BatchEffect
written 4 months ago by • 0
4
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7
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1.3k
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What does evidence of batch effect in bulk rnaseq look like?
surrogatevariables DESeq2 BatchEffect bulkrna-seq sva-seq
updated 5 months ago by ▴ 10 • written 6 months ago by ▴ 70
2
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2
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574
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Control group between 2 batches have different expression in RNAseq data
BatchQC BatchEffect rnaseqGene Normalization
updated 7 months ago by ▴ 10 • written 8 months ago by • 0
2
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2
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670
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How to remove batch effect to combine RNAseq data from 2 different experiments?
BatchQC BatchEffect RNASeq
updated 7 months ago by ▴ 10 • written 8 months ago by • 0
0
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1
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399
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ReactomeGSA for RNASeq
ReactomeGSA BatchEffect RNASeqData
updated 4 months ago by ▴ 20 • written 8 months ago by • 0
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1.1k
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Batch effect correction: methylome data
sesame BatchEffect MethylationArray
updated 8 months ago by ▴ 20 • written 8 months ago by • 0
2
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9
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1.1k
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Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2 RUVSeq RUVseq BatchEffect DES
updated 9 months ago by 67k • written 9 months ago by • 0
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2
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653
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RNAseq:Technical replicates from different batches
technicalReplicates BatchEffect limma RNASeq
9 months ago catv • 0
0
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8
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923
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DESeq and SVA for batch effect
DESeq2 BatchEffect sva
10 months ago michelafrancesconi8 • 0
1
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3
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741
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DESEQ2 Batch Effect
DESeq2 BatchEffect RNASeq
updated 10 months ago by ★ 1.4k • written 10 months ago by ▴ 10
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0
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398
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Can I combine collinear variables into a single value
BatchEffect limma
10 months ago Harrsha • 0
2
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1
reply
526
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Limma Question
DESeq2 BatchEffect limma RNASeq
updated 11 months ago by 43k • written 11 months ago by ▴ 10
4
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1
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1.1k
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When should I correct for batch effects
BatchEffect SingleCellExperiment
updated 12 months ago by 67k • written 12 months ago by ▴ 20
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1.4k
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Can SVs identified from sva be used for removeBatchEffect() in DESeq2
sva DESeq2 BatchEffect limma
updated 12 months ago by ★ 4.6k • written 12 months ago by • 0
2
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4
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1.3k
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Correct the batch effect in methylation analysis in R
BatchEffect limma methylationArrayAnalysis
updated 13 months ago by 52k • written 13 months ago by • 0
1
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1.0k
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controling for batch effect while preserving variation within repeated measures that unevenly distributed across batches
miRNA BatchEffect RNASeq limma
14 months ago Wending • 0
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4
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1.0k
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How to correct for known and surrogate variables in DESeq2?
DESeq2 BatchEffect sva limma
updated 9 months ago by 43k • written 15 months ago by • 0
0
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1
reply
679
views
Batch effect adjust in model matrix
BatchEffect edgeR
updated 16 months ago by ★ 4.6k • written 16 months ago by • 0
3
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5
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1.6k
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Getting batch corrected counts after RUVSeq
BatchEffect RUVSeq RNASeq DESeq2
updated 16 months ago by ★ 4.6k • written 16 months ago by • 0
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5
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removing the batch effect for vst counts and defining the batches in removeBatchEffect function
DESeq2 BatchEffect limma
updated 17 months ago by 52k • written 17 months ago by • 0
2
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3
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2.1k
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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 17 months ago by 67k • written 17 months ago by ▴ 10
3
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4
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1.3k
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lfcShrink() and batch effects in DESeq2
BatchEffect lfcshrink RNA-seq DESeq2
17 months ago Eva ▴ 10
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2
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911
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smallRNA-seq analysis batch correction in limma
BatchEffect limma
18 months ago Eleonora • 0
1
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1
reply
655
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Best way to handle batch effects from difference Mice?
RNASeqData BatchEffect edgeR limma
updated 18 months ago by 52k • written 18 months ago by • 0
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3
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2.0k
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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 19 months ago by ★ 4.6k • written 19 months ago by ▴ 10
0
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0
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609
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How to go for Batch correction in RNA-seq expeiment conducted based on imbalanced Experimental design ?
RNASeqData BatchEffect sva
19 months ago amnahsiddiqa ▴ 10
1
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1
reply
721
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WGCNA Cluster batch effect
BatchEffect TCGA WGCNA
updated 19 months ago by ★ 4.6k • written 19 months ago by • 0
2
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5
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1.8k
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DESeq2 remove batch effect
BatchEffect RNASeqData WGCNA DESeq2
updated 9 months ago by • 0 • written 19 months ago by • 0
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2
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1.5k
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Batch effect between biological replicates
BatchEffect DESeq2
20 months ago gtechbio ▴ 10
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4
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1.4k
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Combine RNA-seq
BatchEffect R rnaseq
updated 21 months ago by ★ 1.4k • written 21 months ago by • 0
2
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4
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2.0k
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How to get TPM / FPKM after batch correction with DESeq2?
DESeq2 BatchEffect tpm fpkm
21 months ago vk • 0
2
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2
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1.3k
views
Error in checkFullRank(modelMatrix)
DESeq2 BatchEffect DifferentialExpression
updated 21 months ago by ★ 4.6k • written 21 months ago by ▴ 30
2
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3
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1.3k
views
Batch correction and Deseq2
DESeq2 WGCNA Normalization NormalyzerDE BatchEffect
updated 22 months ago by ★ 4.6k • written 22 months ago by ▴ 20
2
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1
reply
942
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How to identify the batch informations from the sample ID?
TCGAbiolinks BatchQC BatchEffect
updated 17 months ago by • 0 • written 22 months ago by ▴ 200
3
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2
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1.1k
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Batch question Bulk RNA-Seq
BatchEffect RNASeq
22 months ago chf • 0
2
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1
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2.5k
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DESeq2 design after combatseq batch correction
DESeq2 BatchEffect
updated 23 months ago by ★ 4.6k • written 23 months ago by • 0
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1
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641
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Analysis with Batch correction
DESeq2 BatchEffect
updated 23 months ago by 43k • written 23 months ago by • 0
1
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1
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1.1k
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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 23 months ago by 67k • written 23 months ago by • 0
5
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2
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1.1k
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Sva and batch effect
limma BatchEffect sva
updated 24 months ago by 52k • written 24 months ago by • 0
1
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1
reply
3.3k
views
batch effect correction before DESeq2 analysis
DESeq2 BatchEffect
updated 24 months ago by ★ 4.6k • written 24 months ago by ▴ 50
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0
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1.1k
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Trying to use a NanoString expression set with batch effects to do GSVA
GSVA Normalization BatchEffect GSVAdata NanoString
2.0 years ago Zhijie • 0
1
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0
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968
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Use scran's normalization by deconvolution for each individual sample or over all samples
scran Normalization scRNA BatchEffect
2.1 years ago r_grau ▴ 10
50 results • Page 1 of 1
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Comment: Is there a way to do DEG analysis across two batches sharing one sample only? by georgeyu703 • 0
Michael, Thank you very much!
Comment: Is there a way to do DEG analysis across two batches sharing one sample only? by Michael Love 43k
Yes, with the knowledge that, it is expected to be underpowered.
Comment: Is there a way to do DEG analysis across two batches sharing one sample only? by georgeyu703 • 0
Thank you, Michael. How? Could you provide more details? Can I just do it as usual, I mean to include batch in the model?
Answer: Is there a way to do DEG analysis across two batches sharing one sample only? by Michael Love 43k
The short answer is yes, you can use even a single sample to estimate the batch effect (and therefore control for it in otherwise confounde…
Comment: How to sort negative log2FC or FC in RNAseq for GSEA? by alserg ▴ 280
`NES > 0` means that your gene set has more genes with positive logFC/stat. In your case these genes should be up in Subset1. However, if y…
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Answer: SingleCellExperiment convenience function for metadata+expression?
How to correct for tumor purity using DESeq2 to analyze TCGA tumor sample expression.
Answer: EdgeR Biological CVs
Answer: Error in download.file for TCGAutils::symbolsToRanges
Answer: Error in download.file for TCGAutils::symbolsToRanges
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