Showing : Batcheffect • reset
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Batch correction for microarray
BatchEffect sva MicroarrayData
6 days ago Shaimaa Gamal • 0
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5
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424
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Is there a way to do DEG analysis across two batches sharing one sample only?
DESeq2 DifferentialExpression RNASeqData BatchEffect
written 3 months ago by • 0
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9
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1.2k
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Why did PCA plots look exactly the same after adjusting for batch covariate in DESeq2 design?
DESeq2 BatchEffect
3 months ago Quang NN ▴ 10
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4
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2.0k
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Differential Expression Analysis with unbalanced batches without replication between conditions
edgeR BatchEffect
updated 5 months ago by 52k • written 5 months ago by • 0
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2
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841
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Integration of Single Cell Experiments with batchelor::fastMNN
fastMNN SingleCellData BatchEffect batchelor
6 months ago José • 0
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6
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1.1k
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[DESeq2] Introduce a bias in DESeq2
DifferentialExpression DESeq2 BatchEffect
updated 6 months ago by 43k • written 6 months ago by • 0
5
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4
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742
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How to control batch effect if Group and batch are same?
limma DESeq2 BatchEffect
updated 6 months ago by ★ 4.8k • written 6 months ago by • 0
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5
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994
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heatmap with batch effect
DESeq2 BatchEffect
6 months ago tothuhien • 0
2
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2
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534
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Batch adjustment for cohort based RNA seq data
RNASeqPower removeBatchEffect cpm Batcheffect
7 months ago sukeshinik5 ▴ 20
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2
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519
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ReactomeGSA adjustment for confounding variables
BiologicalQuestion ReactomeGSA BatchEffect
written 7 months ago by • 0
4
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7
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1.8k
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What does evidence of batch effect in bulk rnaseq look like?
surrogatevariables DESeq2 BatchEffect bulkrna-seq sva-seq
updated 8 months ago by ▴ 10 • written 9 months ago by ▴ 70
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2
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687
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Control group between 2 batches have different expression in RNAseq data
BatchQC BatchEffect rnaseqGene Normalization
updated 10 months ago by ▴ 10 • written 11 months ago by • 0
2
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2
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803
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How to remove batch effect to combine RNAseq data from 2 different experiments?
BatchQC BatchEffect RNASeq
updated 10 months ago by ▴ 10 • written 11 months ago by • 0
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1
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485
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ReactomeGSA for RNASeq
ReactomeGSA BatchEffect RNASeqData
updated 7 months ago by ▴ 20 • written 11 months ago by • 0
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2
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1.7k
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Batch effect correction: methylome data
sesame BatchEffect MethylationArray
updated 11 months ago by ▴ 20 • written 11 months ago by • 0
2
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9
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1.4k
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Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2 RUVSeq RUVseq BatchEffect DES
updated 12 months ago by 68k • written 12 months ago by • 0
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2
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897
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RNAseq:Technical replicates from different batches
technicalReplicates BatchEffect limma RNASeq
12 months ago catv • 0
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8
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1.1k
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DESeq and SVA for batch effect
DESeq2 BatchEffect sva
13 months ago michelafrancesconi8 • 0
1
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3
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855
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DESEQ2 Batch Effect
DESeq2 BatchEffect RNASeq
updated 13 months ago by ★ 1.4k • written 14 months ago by ▴ 10
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469
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Can I combine collinear variables into a single value
BatchEffect limma
14 months ago Harrsha • 0
2
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1
reply
600
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Limma Question
DESeq2 BatchEffect limma RNASeq
updated 14 months ago by 43k • written 14 months ago by ▴ 10
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1
reply
1.5k
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When should I correct for batch effects
BatchEffect SingleCellExperiment
updated 15 months ago by 68k • written 15 months ago by ▴ 20
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5
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1.6k
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Can SVs identified from sva be used for removeBatchEffect() in DESeq2
sva DESeq2 BatchEffect limma
updated 15 months ago by ★ 4.8k • written 15 months ago by • 0
2
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4
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1.5k
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Correct the batch effect in methylation analysis in R
BatchEffect limma methylationArrayAnalysis
updated 16 months ago by 52k • written 16 months ago by • 0
1
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4
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1.2k
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controling for batch effect while preserving variation within repeated measures that unevenly distributed across batches
miRNA BatchEffect RNASeq limma
18 months ago Wending • 0
0
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4
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1.2k
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How to correct for known and surrogate variables in DESeq2?
DESeq2 BatchEffect sva limma
updated 12 months ago by 43k • written 18 months ago by • 0
0
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1
reply
734
views
Batch effect adjust in model matrix
BatchEffect edgeR
updated 19 months ago by ★ 4.8k • written 19 months ago by • 0
3
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5
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1.8k
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Getting batch corrected counts after RUVSeq
BatchEffect RUVSeq RNASeq DESeq2
updated 19 months ago by ★ 4.8k • written 19 months ago by • 0
2
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5
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2.4k
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removing the batch effect for vst counts and defining the batches in removeBatchEffect function
DESeq2 BatchEffect limma
updated 20 months ago by 52k • written 20 months ago by • 0
2
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3
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2.6k
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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 20 months ago by 68k • written 20 months ago by ▴ 10
3
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4
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1.6k
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lfcShrink() and batch effects in DESeq2
BatchEffect lfcshrink RNA-seq DESeq2
20 months ago Eva ▴ 10
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2
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1.0k
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smallRNA-seq analysis batch correction in limma
BatchEffect limma
21 months ago Eleonora • 0
1
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1
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711
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Best way to handle batch effects from difference Mice?
RNASeqData BatchEffect edgeR limma
updated 22 months ago by 52k • written 22 months ago by • 0
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3
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2.3k
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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 22 months ago by ★ 4.8k • written 22 months ago by ▴ 10
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0
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691
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How to go for Batch correction in RNA-seq expeiment conducted based on imbalanced Experimental design ?
RNASeqData BatchEffect sva
22 months ago amnahsiddiqa ▴ 10
1
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1
reply
791
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WGCNA Cluster batch effect
BatchEffect TCGA WGCNA
updated 22 months ago by ★ 4.8k • written 22 months ago by • 0
2
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5
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2.0k
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DESeq2 remove batch effect
BatchEffect RNASeqData WGCNA DESeq2
updated 12 months ago by • 0 • written 22 months ago by • 0
1
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2
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1.6k
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Batch effect between biological replicates
BatchEffect DESeq2
23 months ago gtechbio ▴ 10
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4
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1.5k
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Combine RNA-seq
BatchEffect R rnaseq
updated 2.0 years ago by ★ 1.4k • written 2.0 years ago by • 0
2
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4
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2.3k
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How to get TPM / FPKM after batch correction with DESeq2?
DESeq2 BatchEffect tpm fpkm
2.0 years ago vk • 0
2
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2
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1.5k
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Error in checkFullRank(modelMatrix)
DESeq2 BatchEffect DifferentialExpression
updated 2.0 years ago by ★ 4.8k • written 2.0 years ago by ▴ 30
2
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3
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1.5k
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Batch correction and Deseq2
DESeq2 WGCNA Normalization NormalyzerDE BatchEffect
updated 2.1 years ago by ★ 4.8k • written 2.1 years ago by ▴ 20
2
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1
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1.1k
views
How to identify the batch informations from the sample ID?
TCGAbiolinks BatchQC BatchEffect
updated 20 months ago by • 0 • written 2.1 years ago by ▴ 200
3
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2
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1.3k
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Batch question Bulk RNA-Seq
BatchEffect RNASeq
2.1 years ago chf • 0
2
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1
reply
2.9k
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DESeq2 design after combatseq batch correction
DESeq2 BatchEffect
updated 2.2 years ago by ★ 4.8k • written 2.2 years ago by • 0
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1
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701
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Analysis with Batch correction
DESeq2 BatchEffect
updated 2.2 years ago by 43k • written 2.2 years ago by • 0
1
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1
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1.2k
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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 2.2 years ago by 68k • written 2.2 years ago by • 0
5
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2
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1.2k
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Sva and batch effect
limma BatchEffect sva
updated 2.2 years ago by 52k • written 2.2 years ago by • 0
1
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1
reply
4.3k
views
batch effect correction before DESeq2 analysis
DESeq2 BatchEffect
updated 2.2 years ago by ★ 4.8k • written 2.2 years ago by ▴ 50
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0
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Trying to use a NanoString expression set with batch effects to do GSVA
GSVA Normalization BatchEffect GSVAdata NanoString
2.3 years ago Zhijie • 0
50 results • Page 1 of 1
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Replies
Comment: DiffBind; Error: No sites have activity greater than filter value by etiennedanis • 0
Same issue here as well. This is very weird because I never had this issue before. I started observing this issue with a new ATAC-seq da…
Comment: GSEA preranked analysis downstream of DEseq2 by Ajay • 0
`logFC * -log10(pval)` seems to be the pi-score proposed in this [paper][1] [1]: https://pmc.ncbi.nlm.nih.gov/articles/PMC3957066/
Comment: error in ChAMP loading file by janwilseo • 0
Any update on this post? I also had an issue with this. [erosion control](https://charlestonhydroseeding.com/)
Answer: CluserProfiler message "No gene can be mapped" by James W. MacDonald 68k
Two things. First, the order of your term2gene is backwards (should be term and then gene, like the name), and by default `enricher` adjust…
Comment: Controlling for batch and estrus cycle using DESeq2 in RNA-seq analysis by donnycrimson • 0
One potential workaround might be to adjust for these factors using a combination of design matrices perhaps including batch as a covariate…
Votes
Answer: DiffBind; Error: No sites have activity greater than filter value
DiffBind; Error: No sites have activity greater than filter value
remove X and Y chromosome genes in RNA-seq data using DESeq2 pipeline
How to remove X & Y chromosome genes from RNAseq data
Is it advisable to remove X and Y chromosome genes in mouse bulk RNA-seq data at the level of the count matrix?
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