Showing : Batcheffect • reset
0
votes
0
replies
396
views
Batch correction for microarray
BatchEffect sva MicroarrayData
8 months ago Shaimaa Gamal • 0
0
votes
5
replies
778
views
Is there a way to do DEG analysis across two batches sharing one sample only?
DESeq2 DifferentialExpression RNASeqData BatchEffect
written 11 months ago by • 0
2
votes
9
replies
1.8k
views
Why did PCA plots look exactly the same after adjusting for batch covariate in DESeq2 design?
DESeq2 BatchEffect
12 months ago • updated 11 months ago Quang NN ▴ 10
2
votes
4
replies
2.6k
views
Differential Expression Analysis with unbalanced batches without replication between conditions
edgeR BatchEffect
updated 14 months ago by 53k • written 14 months ago by • 0
0
votes
2
replies
1.2k
views
Integration of Single Cell Experiments with batchelor::fastMNN
fastMNN SingleCellData BatchEffect batchelor
14 months ago José • 0
0
votes
6
replies
1.5k
views
[DESeq2] Introduce a bias in DESeq2
DifferentialExpression DESeq2 BatchEffect
updated 14 months ago by 43k • written 15 months ago by • 0
5
votes
4
replies
1.1k
views
How to control batch effect if Group and batch are same?
limma DESeq2 BatchEffect
updated 15 months ago by ★ 5.0k • written 15 months ago by • 0
1
vote
6
replies
1.5k
views
heatmap with batch effect
DESeq2 BatchEffect
written 15 months ago by • 0
2
votes
2
replies
788
views
Batch adjustment for cohort based RNA seq data
RNASeqPower removeBatchEffect cpm Batcheffect
15 months ago sukeshinik5 ▴ 20
0
votes
2
replies
747
views
ReactomeGSA adjustment for confounding variables
BiologicalQuestion ReactomeGSA BatchEffect
written 16 months ago by • 0
4
votes
7
replies
2.4k
views
What does evidence of batch effect in bulk rnaseq look like?
surrogatevariables DESeq2 BatchEffect bulkrna-seq sva-seq
updated 17 months ago by ▴ 10 • written 18 months ago by ▴ 70
2
votes
2
replies
930
views
Control group between 2 batches have different expression in RNAseq data
BatchQC BatchEffect rnaseqGene Normalization
updated 19 months ago by ▴ 10 • written 19 months ago by • 0
2
votes
2
replies
1.1k
views
How to remove batch effect to combine RNAseq data from 2 different experiments?
BatchQC BatchEffect RNASeq
updated 19 months ago by ▴ 10 • written 19 months ago by • 0
0
votes
1
reply
768
views
ReactomeGSA for RNASeq
ReactomeGSA BatchEffect RNASeqData
updated 16 months ago by ▴ 20 • written 20 months ago by • 0
0
votes
2
replies
2.3k
views
Batch effect correction: methylome data
sesame BatchEffect MethylationArray
updated 20 months ago by ▴ 20 • written 20 months ago by • 0
2
votes
9
replies
1.9k
views
Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2 RUVSeq RUVseq BatchEffect DES
updated 20 months ago by 68k • written 20 months ago by • 0
0
votes
2
replies
1.3k
views
RNAseq:Technical replicates from different batches
technicalReplicates BatchEffect limma RNASeq
20 months ago catv • 0
0
votes
8
replies
1.6k
views
DESeq and SVA for batch effect
DESeq2 BatchEffect sva
22 months ago michelafrancesconi8 • 0
1
vote
3
replies
1.1k
views
DESEQ2 Batch Effect
DESeq2 BatchEffect RNASeq
updated 22 months ago by ★ 1.4k • written 22 months ago by ▴ 10
0
votes
0
replies
602
views
Can I combine collinear variables into a single value
BatchEffect limma
22 months ago Harrsha • 0
2
votes
1
reply
773
views
Limma Question
DESeq2 BatchEffect limma RNASeq
updated 22 months ago by 43k • written 22 months ago by ▴ 10
4
votes
1
reply
1.9k
views
When should I correct for batch effects
BatchEffect SingleCellExperiment
updated 23 months ago by 68k • written 23 months ago by ▴ 20
0
votes
5
replies
2.0k
views
Can SVs identified from sva be used for removeBatchEffect() in DESeq2
sva DESeq2 BatchEffect limma
updated 2.0 years ago by ★ 5.0k • written 2.0 years ago by • 0
2
votes
4
replies
1.8k
views
Correct the batch effect in methylation analysis in R
BatchEffect limma methylationArrayAnalysis
updated 2.1 years ago by 53k • written 2.1 years ago by • 0
1
vote
4
replies
1.6k
views
controling for batch effect while preserving variation within repeated measures that unevenly distributed across batches
miRNA BatchEffect RNASeq limma
2.2 years ago Wending • 0
0
votes
4
replies
1.4k
views
How to correct for known and surrogate variables in DESeq2?
DESeq2 BatchEffect sva limma
updated 21 months ago by 43k • written 2.2 years ago by • 0
0
votes
1
reply
877
views
Batch effect adjust in model matrix
BatchEffect edgeR
updated 2.3 years ago by ★ 5.0k • written 2.3 years ago by • 0
3
votes
5
replies
2.3k
views
Getting batch corrected counts after RUVSeq
BatchEffect RUVSeq RNASeq DESeq2
updated 2.3 years ago by ★ 5.0k • written 2.3 years ago by • 0
2
votes
5
replies
2.9k
views
removing the batch effect for vst counts and defining the batches in removeBatchEffect function
DESeq2 BatchEffect limma
updated 2.4 years ago by 53k • written 2.4 years ago by • 0
2
votes
3
replies
3.2k
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 2.4 years ago by 68k • written 2.4 years ago by ▴ 10
3
votes
4
replies
2.1k
views
lfcShrink() and batch effects in DESeq2
BatchEffect lfcshrink RNA-seq DESeq2
2.4 years ago Eva ▴ 10
0
votes
2
replies
1.2k
views
smallRNA-seq analysis batch correction in limma
BatchEffect limma
2.5 years ago Eleonora • 0
1
vote
1
reply
842
views
Best way to handle batch effects from difference Mice?
RNASeqData BatchEffect edgeR limma
updated 2.5 years ago by 53k • written 2.5 years ago by • 0
2
votes
3
replies
2.6k
views
PCA for QC should include subset of top variable genes or full set of genes in RNAseq data?
BatchQC RNASeqData sva BatchEffect
updated 2.5 years ago by ★ 5.0k • written 2.5 years ago by ▴ 10
0
votes
0
replies
897
views
How to go for Batch correction in RNA-seq expeiment conducted based on imbalanced Experimental design ?
RNASeqData BatchEffect sva
2.5 years ago amnahsiddiqa ▴ 10
1
vote
1
reply
975
views
WGCNA Cluster batch effect
BatchEffect TCGA WGCNA
updated 2.5 years ago by ★ 5.0k • written 2.5 years ago by • 0
2
votes
5
replies
2.4k
views
DESeq2 remove batch effect
BatchEffect RNASeqData WGCNA DESeq2
updated 21 months ago by • 0 • written 2.6 years ago by • 0
1
vote
2
replies
1.8k
views
Batch effect between biological replicates
BatchEffect DESeq2
2.7 years ago • updated 2.6 years ago gtechbio ▴ 10
0
votes
4
replies
1.8k
views
Combine RNA-seq
BatchEffect R rnaseq
updated 2.7 years ago by ★ 1.4k • written 2.7 years ago by • 0
2
votes
4
replies
2.6k
views
How to get TPM / FPKM after batch correction with DESeq2?
DESeq2 BatchEffect tpm fpkm
2.7 years ago vk • 0
2
votes
2
replies
1.8k
views
Error in checkFullRank(modelMatrix)
DESeq2 BatchEffect DifferentialExpression
updated 2.7 years ago by ★ 5.0k • written 2.7 years ago by ▴ 30
2
votes
3
replies
1.9k
views
Batch correction and Deseq2
DESeq2 WGCNA Normalization NormalyzerDE BatchEffect
updated 2.8 years ago by ★ 5.0k • written 2.8 years ago by ▴ 20
2
votes
1
reply
1.5k
views
How to identify the batch informations from the sample ID?
TCGAbiolinks BatchQC BatchEffect
updated 2.4 years ago by • 0 • written 2.8 years ago by ▴ 200
3
votes
2
replies
1.6k
views
Batch question Bulk RNA-Seq
BatchEffect RNASeq
2.8 years ago chf • 0
2
votes
1
reply
3.3k
views
DESeq2 design after combatseq batch correction
DESeq2 BatchEffect
updated 2.9 years ago by ★ 5.0k • written 2.9 years ago by • 0
0
votes
1
reply
832
views
Analysis with Batch correction
DESeq2 BatchEffect
updated 2.9 years ago by 43k • written 2.9 years ago by • 0
1
vote
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 2.9 years ago by 68k • written 2.9 years ago by • 0
5
votes
2
replies
1.4k
views
Sva and batch effect
limma BatchEffect sva
updated 2.9 years ago by 53k • written 2.9 years ago by • 0
1
vote
1
reply
4.9k
views
batch effect correction before DESeq2 analysis
DESeq2 BatchEffect
updated 2.9 years ago by ★ 5.0k • written 2.9 years ago by ▴ 50
0
votes
0
replies
1.5k
views
Trying to use a NanoString expression set with batch effects to do GSVA
GSVA Normalization BatchEffect GSVAdata NanoString
3.0 years ago Zhijie • 0
93 results • Page 1 of 2
Recent ...
Replies
Comment: Guitar R package requires update due to dependency GenomicFeatures by ferran.llobet.cabau ▴ 10
Thank you @seandavi for your feedback. I followed your recommendations and generated a [pull request][1] including the fix for this issue…
Comment: Ensembl plants at annotationHub? by Guido Hooiveld ★ 4.1k
Hope you don't mind I am not Johannes... ;-) Note that you nowadays can generate these yourselves using the `docker` image Johannes made av…
Comment: How does contrasts.fit do in limma to extract comparisons with a model having in by jtsy6383 • 0
Thanks for the reminder about DiffVar (for that project I ended up using GAMLSS in the end and haven't touched DiffVar since) and the alter…
Comment: Ensembl plants at annotationHub? by jwp48 • 0
Dear Johannes, Would it be possible to generate a EnsDb for the newest Medicago V5 genome release? Medicago truncatula A17 r5.0 This woul…
Answer: please provide a BibTeX citation for "Advanced Single-Cell Analysis with Biocond by Ludwig Geistlinger ▴ 80
When referring to the OSCA book including individual sub-books please cite the OSCA paper: Amezquita, R.A., Lun, A.T.L., Becht, E. et a…
Votes
limma moderated t-statistics and B-statistics
Comment: Guitar R package requires update due to dependency GenomicFeatures
A: how to control age and gender effect in expression data using DESeq2
A: how to control age and gender effect in expression data using DESeq2
how to control age and gender effect in expression data using DESeq2
Awards • All
Popular Question to Gordon Smyth 53k
Popular Question to Aleena_Ensembl ▴ 30
Popular Question to Hervé Pagès 16k
Teacher to Michael Love 43k
Popular Question to lianov • 0
Locations • All
The city by the bay, 7 minutes ago
Australia, 26 minutes ago
United States, 1 hour ago
The Netherlands, 2 hours ago
United States, 3 hours ago
Traffic: 1958 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6