Showing : Batcheffect • reset
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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 10 weeks ago by • 0
2
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9
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1.1k
views
Why did PCA plots look exactly the same after adjusting for batch covariate in DESeq2 design?
DESeq2 BatchEffect
12 weeks ago • updated 10 weeks ago Quang NN ▴ 10
2
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4
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1.9k
views
Differential Expression Analysis with unbalanced batches without replication between conditions
edgeR BatchEffect
updated 4 months ago by 52k • written 5 months ago by • 0
0
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2
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775
views
Integration of Single Cell Experiments with batchelor::fastMNN
fastMNN SingleCellData BatchEffect batchelor
5 months ago José • 0
0
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6
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1.1k
views
[DESeq2] Introduce a bias in DESeq2
DifferentialExpression DESeq2 BatchEffect
updated 5 months ago by 43k • written 6 months ago by • 0
5
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4
replies
682
views
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
0
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5
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926
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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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500
views
Batch adjustment for cohort based RNA seq data
RNASeqPower removeBatchEffect cpm Batcheffect
6 months ago sukeshinik5 ▴ 20
0
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2
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503
views
ReactomeGSA adjustment for confounding variables
BiologicalQuestion ReactomeGSA BatchEffect
written 7 months ago by • 0
4
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7
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1.6k
views
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
2
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2
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668
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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 10 months ago by • 0
2
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2
replies
778
views
How to remove batch effect to combine RNAseq data from 2 different experiments?
BatchQC BatchEffect RNASeq
updated 10 months ago by ▴ 10 • written 10 months ago by • 0
0
votes
1
reply
471
views
ReactomeGSA for RNASeq
ReactomeGSA BatchEffect RNASeqData
updated 7 months ago by ▴ 20 • written 10 months ago by • 0
0
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2
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1.5k
views
Batch effect correction: methylome data
sesame BatchEffect MethylationArray
updated 10 months ago by ▴ 20 • written 10 months ago by • 0
2
votes
9
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1.3k
views
Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2 RUVSeq RUVseq BatchEffect DES
updated 11 months ago by 68k • written 11 months ago by • 0
0
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2
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828
views
RNAseq:Technical replicates from different batches
technicalReplicates BatchEffect limma RNASeq
11 months ago catv • 0
0
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8
replies
1.1k
views
DESeq and SVA for batch effect
DESeq2 BatchEffect sva
13 months ago michelafrancesconi8 • 0
1
vote
3
replies
836
views
DESEQ2 Batch Effect
DESeq2 BatchEffect RNASeq
updated 13 months ago by ★ 1.4k • written 13 months ago by ▴ 10
0
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0
replies
455
views
Can I combine collinear variables into a single value
BatchEffect limma
13 months ago Harrsha • 0
2
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1
reply
586
views
Limma Question
DESeq2 BatchEffect limma RNASeq
updated 13 months ago by 43k • written 13 months ago by ▴ 10
4
votes
1
reply
1.4k
views
When should I correct for batch effects
BatchEffect SingleCellExperiment
updated 14 months ago by 68k • written 14 months ago by ▴ 20
0
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5
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1.6k
views
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
replies
1.4k
views
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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1.1k
views
controling for batch effect while preserving variation within repeated measures that unevenly distributed across batches
miRNA BatchEffect RNASeq limma
17 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 11 months ago by 43k • written 17 months ago by • 0
0
votes
1
reply
719
views
Batch effect adjust in model matrix
BatchEffect edgeR
updated 18 months ago by ★ 4.8k • written 18 months ago by • 0
3
votes
5
replies
1.7k
views
Getting batch corrected counts after RUVSeq
BatchEffect RUVSeq RNASeq DESeq2
updated 19 months ago by ★ 4.8k • written 19 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 20 months ago by 52k • written 20 months ago by • 0
2
votes
3
replies
2.4k
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 20 months ago by 68k • written 20 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
20 months ago Eva ▴ 10
0
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2
replies
1000
views
smallRNA-seq analysis batch correction in limma
BatchEffect limma
20 months ago Eleonora • 0
1
vote
1
reply
695
views
Best way to handle batch effects from difference Mice?
RNASeqData BatchEffect edgeR limma
updated 21 months ago by 52k • written 21 months ago by • 0
2
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3
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2.2k
views
PCA for QC should include subset of top variable genes or full set of genes in RNAseq data?
BatchQC RNASeqData sva BatchEffect
updated 21 months ago by ★ 4.8k • written 21 months ago by ▴ 10
0
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0
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672
views
How to go for Batch correction in RNA-seq expeiment conducted based on imbalanced Experimental design ?
RNASeqData BatchEffect sva
21 months ago amnahsiddiqa ▴ 10
1
vote
1
reply
775
views
WGCNA Cluster batch effect
BatchEffect TCGA WGCNA
updated 21 months ago by ★ 4.8k • written 21 months ago by • 0
2
votes
5
replies
1.9k
views
DESeq2 remove batch effect
BatchEffect RNASeqData WGCNA DESeq2
updated 11 months ago by • 0 • written 22 months ago by • 0
1
vote
2
replies
1.6k
views
Batch effect between biological replicates
BatchEffect DESeq2
23 months ago • updated 22 months ago gtechbio ▴ 10
0
votes
4
replies
1.5k
views
Combine RNA-seq
BatchEffect R rnaseq
updated 23 months ago by ★ 1.4k • written 23 months ago by • 0
2
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4
replies
2.2k
views
How to get TPM / FPKM after batch correction with DESeq2?
DESeq2 BatchEffect tpm fpkm
24 months ago vk • 0
2
votes
2
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1.5k
views
Error in checkFullRank(modelMatrix)
DESeq2 BatchEffect DifferentialExpression
updated 24 months ago by ★ 4.8k • written 24 months ago by ▴ 30
2
votes
3
replies
1.5k
views
Batch correction and Deseq2
DESeq2 WGCNA Normalization NormalyzerDE BatchEffect
updated 2.0 years ago by ★ 4.8k • written 2.1 years ago by ▴ 20
2
votes
1
reply
1.1k
views
How to identify the batch informations from the sample ID?
TCGAbiolinks BatchQC BatchEffect
updated 19 months ago by • 0 • written 2.1 years ago by ▴ 200
3
votes
2
replies
1.3k
views
Batch question Bulk RNA-Seq
BatchEffect RNASeq
2.1 years ago chf • 0
2
votes
1
reply
2.8k
views
DESeq2 design after combatseq batch correction
DESeq2 BatchEffect
updated 2.1 years ago by ★ 4.8k • written 2.1 years ago by • 0
0
votes
1
reply
690
views
Analysis with Batch correction
DESeq2 BatchEffect
updated 2.1 years ago by 43k • written 2.1 years ago by • 0
1
vote
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
1.2k
views
Sva and batch effect
limma BatchEffect sva
updated 2.2 years ago by 52k • written 2.2 years ago by • 0
1
vote
1
reply
4.0k
views
batch effect correction before DESeq2 analysis
DESeq2 BatchEffect
updated 2.2 years ago by ★ 4.8k • written 2.2 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
2.3 years ago Zhijie • 0
1
vote
0
replies
1.1k
views
Use scran's normalization by deconvolution for each individual sample or over all samples
scran Normalization scRNA BatchEffect
2.3 years ago r_grau ▴ 10
50 results • Page 1 of 1
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Comment: DESeq2 - human data, weird results, troubleshooting by bd2000 ▴ 30
I didn't include all of my code the post would be too long. Here's a link to my GitHub if anyone would like to see the full code: [Full Rst…
Answer: DESeq: Gene is not flagged as differentially expressed despite count data showin by James W. MacDonald 68k
The simple answer is that the within-group variability is much higher for the first gene as compared to the second. The Wald statistic is j…
Comment: DESeq: Gene is not flagged as differentially expressed despite count data showin by ATpoint ★ 4.8k
> since there doesn't seem to be as much count variability, No? Your CD45 samples range on normalized scale from 2 to 3255. That's 3 orde…
Comment: Ensembl site unresponsive via biomaRt by darylruiz6545 • 0
Thank you so much for sharing the link.
Comment: compute_fasta_digest does not match Salmon index hash by Alex • 0
I use the `fastaDigest` tool from [COMBINE-lab/fastaDigest](https://github.com/COMBINE-lab/FastaDigest/), which has the function `compute_f…
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Answer: DESeq: Gene is not flagged as differentially expressed despite count data showin
Two EPIC Methylation Array Analysis Questions
How to get DMR for Infinium methylation EPIC v2
A: GEOquery Fails to Download Series Matrix File
Comment: Gene IDs conversion between Ensembl and NCBI nomenclature for non-model species
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