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 4 weeks ago by • 0
2
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9
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908
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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
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4
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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
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2
replies
667
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Integration of Single Cell Experiments with batchelor::fastMNN
fastMNN SingleCellData BatchEffect batchelor
4 months ago José • 0
0
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6
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944
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[DESeq2] Introduce a bias in DESeq2
DifferentialExpression DESeq2 BatchEffect
updated 3 months ago by 43k • written 4 months ago by • 0
5
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4
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572
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
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5
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787
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heatmap with batch effect
DESeq2 BatchEffect
4 months ago tothuhien • 0
2
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2
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425
views
Batch adjustment for cohort based RNA seq data
RNASeqPower removeBatchEffect cpm Batcheffect
5 months ago sukeshinik5 ▴ 20
0
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2
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457
views
ReactomeGSA adjustment for confounding variables
BiologicalQuestion ReactomeGSA BatchEffect
written 5 months ago by • 0
4
votes
7
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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
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2
replies
718
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
433
views
ReactomeGSA for RNASeq
ReactomeGSA BatchEffect RNASeqData
updated 5 months ago by ▴ 20 • written 9 months ago by • 0
0
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2
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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
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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
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2
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720
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RNAseq:Technical replicates from different batches
technicalReplicates BatchEffect limma RNASeq
10 months ago catv • 0
0
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8
replies
981
views
DESeq and SVA for batch effect
DESeq2 BatchEffect sva
11 months ago michelafrancesconi8 • 0
1
vote
3
replies
786
views
DESEQ2 Batch Effect
DESeq2 BatchEffect RNASeq
updated 11 months ago by ★ 1.4k • written 11 months ago by ▴ 10
0
votes
0
replies
425
views
Can I combine collinear variables into a single value
BatchEffect limma
11 months ago Harrsha • 0
2
votes
1
reply
550
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
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5
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1.5k
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
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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
15 months ago Wending • 0
0
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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
700
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
949
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
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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
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0
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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 2.0 years ago by ★ 4.7k • written 2.0 years 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
2.2 years ago r_grau ▴ 10
50 results • Page 1 of 1
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Comment: Differential variance analysis - can i use deseq2 by Michael Love 43k
VST is valid for working with expression data on a variance stabilized scale, so yes. There are many papers that have used VST and then com…
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
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
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