Showing : BatchEffect • reset
0
votes
5
replies
319
views
Is there a way to do DEG analysis across two batches sharing one sample only?
DESeq2 DifferentialExpression RNASeqData BatchEffect
written 4 weeks ago by • 0
2
votes
9
replies
902
views
Why did PCA plots look exactly the same after adjusting for batch covariate in DESeq2 design?
DESeq2 BatchEffect
6 weeks ago • updated 4 weeks ago Quang NN ▴ 10
2
votes
4
replies
1.8k
views
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
votes
2
replies
665
views
Integration of Single Cell Experiments with batchelor::fastMNN
fastMNN SingleCellData BatchEffect batchelor
4 months ago José • 0
0
votes
6
replies
942
views
[DESeq2] Introduce a bias in DESeq2
DifferentialExpression DESeq2 BatchEffect
updated 3 months ago by 43k • written 4 months ago by • 0
5
votes
4
replies
569
views
How to control batch effect if Group and batch are same?
limma DESeq2 BatchEffect
updated 4 months ago by ★ 4.7k • written 4 months ago by • 0
0
votes
5
replies
787
views
heatmap with batch effect
DESeq2 BatchEffect
4 months ago tothuhien • 0
2
votes
2
replies
423
views
Batch adjustment for cohort based RNA seq data
RNASeqPower removeBatchEffect cpm Batcheffect
4 months ago sukeshinik5 ▴ 20
0
votes
2
replies
456
views
ReactomeGSA adjustment for confounding variables
BiologicalQuestion ReactomeGSA BatchEffect
written 5 months ago by • 0
4
votes
7
replies
1.4k
views
What does evidence of batch effect in bulk rnaseq look like?
surrogatevariables DESeq2 BatchEffect bulkrna-seq sva-seq
updated 6 months ago by ▴ 10 • written 7 months ago by ▴ 70
2
votes
2
replies
615
views
Control group between 2 batches have different expression in RNAseq data
BatchQC BatchEffect rnaseqGene Normalization
updated 8 months ago by ▴ 10 • written 9 months ago by • 0
2
votes
2
replies
716
views
How to remove batch effect to combine RNAseq data from 2 different experiments?
BatchQC BatchEffect RNASeq
updated 8 months ago by ▴ 10 • written 9 months ago by • 0
0
votes
1
reply
432
views
ReactomeGSA for RNASeq
ReactomeGSA BatchEffect RNASeqData
updated 5 months ago by ▴ 20 • written 9 months ago by • 0
0
votes
2
replies
1.2k
views
Batch effect correction: methylome data
sesame BatchEffect MethylationArray
updated 9 months ago by ▴ 20 • written 9 months ago by • 0
2
votes
9
replies
1.1k
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
votes
2
replies
718
views
RNAseq:Technical replicates from different batches
technicalReplicates BatchEffect limma RNASeq
10 months ago catv • 0
0
votes
8
replies
978
views
DESeq and SVA for batch effect
DESeq2 BatchEffect sva
11 months ago michelafrancesconi8 • 0
1
vote
3
replies
784
views
DESEQ2 Batch Effect
DESeq2 BatchEffect RNASeq
updated 11 months ago by ★ 1.4k • written 11 months ago by ▴ 10
0
votes
0
replies
424
views
Can I combine collinear variables into a single value
BatchEffect limma
11 months ago Harrsha • 0
2
votes
1
reply
548
views
Limma Question
DESeq2 BatchEffect limma RNASeq
updated 12 months ago by 43k • written 12 months ago by ▴ 10
4
votes
1
reply
1.2k
views
When should I correct for batch effects
BatchEffect SingleCellExperiment
updated 13 months ago by 68k • written 13 months ago by ▴ 20
0
votes
5
replies
1.4k
views
Can SVs identified from sva be used for removeBatchEffect() in DESeq2
sva DESeq2 BatchEffect limma
updated 13 months ago by ★ 4.7k • written 13 months ago by • 0
2
votes
4
replies
1.3k
views
Correct the batch effect in methylation analysis in R
BatchEffect limma methylationArrayAnalysis
updated 14 months ago by 52k • written 14 months ago by • 0
1
vote
4
replies
1.1k
views
controling for batch effect while preserving variation within repeated measures that unevenly distributed across batches
miRNA BatchEffect RNASeq limma
15 months ago Wending • 0
0
votes
4
replies
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
699
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
1.6k
views
Getting batch corrected counts after RUVSeq
BatchEffect RUVSeq RNASeq DESeq2
updated 17 months ago by ★ 4.7k • written 17 months ago by • 0
2
votes
5
replies
2.2k
views
removing the batch effect for vst counts and defining the batches in removeBatchEffect function
DESeq2 BatchEffect limma
updated 18 months ago by 52k • written 18 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 18 months ago by 68k • written 18 months ago by ▴ 10
3
votes
4
replies
1.4k
views
lfcShrink() and batch effects in DESeq2
BatchEffect lfcshrink RNA-seq DESeq2
18 months ago Eva ▴ 10
0
votes
2
replies
948
views
smallRNA-seq analysis batch correction in limma
BatchEffect limma
19 months ago Eleonora • 0
1
vote
1
reply
676
views
Best way to handle batch effects from difference Mice?
RNASeqData BatchEffect edgeR limma
updated 19 months ago by 52k • written 19 months ago by • 0
2
votes
3
replies
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
votes
0
replies
638
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
745
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
1.8k
views
DESeq2 remove batch effect
BatchEffect RNASeqData WGCNA DESeq2
updated 10 months ago by • 0 • written 20 months ago by • 0
1
vote
2
replies
1.5k
views
Batch effect between biological replicates
BatchEffect DESeq2
21 months ago gtechbio ▴ 10
0
votes
4
replies
1.4k
views
Combine RNA-seq
BatchEffect R rnaseq
updated 22 months ago by ★ 1.4k • written 22 months ago by • 0
2
votes
4
replies
2.1k
views
How to get TPM / FPKM after batch correction with DESeq2?
DESeq2 BatchEffect tpm fpkm
22 months ago vk • 0
2
votes
2
replies
1.4k
views
Error in checkFullRank(modelMatrix)
DESeq2 BatchEffect DifferentialExpression
updated 22 months ago by ★ 4.7k • written 22 months ago by ▴ 30
2
votes
3
replies
1.4k
views
Batch correction and Deseq2
DESeq2 WGCNA Normalization NormalyzerDE BatchEffect
updated 23 months ago by ★ 4.7k • written 23 months ago by ▴ 20
2
votes
1
reply
999
views
How to identify the batch informations from the sample ID?
TCGAbiolinks BatchQC BatchEffect
updated 18 months ago by • 0 • written 23 months ago by ▴ 200
3
votes
2
replies
1.2k
views
Batch question Bulk RNA-Seq
BatchEffect RNASeq
23 months ago chf • 0
2
votes
1
reply
2.6k
views
DESeq2 design after combatseq batch correction
DESeq2 BatchEffect
updated 24 months ago by ★ 4.7k • written 24 months ago by • 0
0
votes
1
reply
661
views
Analysis with Batch correction
DESeq2 BatchEffect
updated 2.0 years ago by 43k • written 2.0 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 2.0 years ago by 68k • written 2.0 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
3.6k
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
votes
0
replies
1.1k
views
Trying to use a NanoString expression set with batch effects to do GSVA
GSVA Normalization BatchEffect GSVAdata NanoString
2.1 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
2.1 years ago r_grau ▴ 10
50 results • Page 1 of 1
Recent ...
Replies
Answer: Use of limma R package with targeted proteomics for DE analysis by Gordon Smyth 52k
It is usual to analyse log normalized values from Olink in limma. Just a straight log transformation should be sufficient. We find that `tr…
Comment: WGCNA by pammelala304 • 0
Thank you for your time and effort. I am so grateful! Play game [block blast](https://blockblastpuzzle.io) free.
Comment: Does anyone have the command to download all of the core_nt using blast_db_get() by Matthew Thornton ▴ 380
Ok. So I guess the core_nt is over 300Gb compressed. I can do it, but maybe it is better to just use ncbi-tools over the internet and just…
Comment: normalizatino of dna methylation EPIC data by user_bioinfo • 0
yes actually that's why I did, and its all good! thank you for your response
Comment: batch effect removal for agilent microarray data by gaye.yilmaz • 0
Hello again, Can using inSilicoMerging handle this situation?
Votes
Comment: Different annotation packages (org.Mm.eg.db, EnsDb.Mmusculus.v79, BiomaRt) retu
Answer: normalizatino of dna methylation EPIC data
Answer: Differential expression of protein coding ENSGs (Ensembl IDs) | When to biomaRt?
Suggesting changing the "reply-to" field to the mailing list address.
Answer: UniProt.ws query for single UniRef90 ID takes several minutes
Awards • All
Popular Question to Hugo Varet ▴ 80
Popular Question to Fred Hutch (Recruiting) ▴ 40
Popular Question to Wolfgang Huber ★ 13k
Popular Question to picasa1983 • 0
Popular Question to mahes.muniandy • 0
Locations • All
Germany, 33 minutes ago
WEHI, Melbourne, Australia, 1 hour ago
France, 1 hour ago
South Korea, 1 hour ago
The city by the bay, 1 hour ago
Traffic: 873 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