Showing : Batch effect • reset
3
votes
7
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6.0k
views
limma::removeBatchEffect into DESeq2
deseq2 limma batch effect
updated 4.2 years ago by ★ 4.0k • written 4.2 years ago by • 0
4
votes
5
replies
3.4k
views
How to incorporate batch effect that is only present in one level into the design?
linear model batch effect DESeq2 design
updated 4.2 years ago by 67k • written 4.2 years ago by • 0
2
votes
8
replies
4.9k
views
Remove batch effect limma, "Coefficients not estimable" warning and design matrix
limma deseq2 batch design batch effect
4.2 years ago Pietro ▴ 40
2
votes
2
replies
1.1k
views
edgeR batch effect correction for unevenly distributed groups
rnaseq edgeR batch effect
updated 4.3 years ago by 51k • written 4.3 years ago by • 0
2
votes
5
replies
3.8k
views
Possible batch effect correction with RNA-Seq data when the batches do not contain both biological conditions for DE analysis
batch effect limma rna seq DE
updated 4.6 years ago by ★ 13k • written 4.6 years ago by ▴ 830
0
votes
0
replies
753
views
Concatenating different runs from the same pool of barcoded CyTOF samples
batch effect cytof
4.6 years ago mikhael.manurung ▴ 280
0
votes
10
replies
3.0k
views
DEseq2 design formula correcting for batch
deseq2 design formula batch effect
updated 4.8 years ago by ★ 1.4k • written 4.8 years ago by • 0
0
votes
1
reply
1.1k
views
problem for interpretation of resulted ComBat() plot
ComBat sva batch effect RNA-seq
updated 4.9 years ago by ▴ 860 • written 4.9 years ago by ▴ 10
1
vote
4
replies
1.9k
views
edgeR design matrix for 2 variables + batch effect
egdeR design matrix batch effect
updated 5.0 years ago by 51k • written 5.0 years ago by • 0
3
votes
2
replies
2.1k
views
Variation between technical replicates (DESeq2, batch effects)
rnaseq deseq2 differential expression batch effect replicates
updated 5.1 years ago by 42k • written 5.1 years ago by ▴ 10
1
vote
2
replies
1.1k
views
The order used in common practce? batch effect removel and normalization
normalization batch effect
updated 5.1 years ago by ▴ 420 • written 5.1 years ago by ▴ 10
2
votes
3
replies
1.3k
views
Design for introducing batch effect in DESeq2
deseq2 combat batch effect rna-seq edger
updated 5.2 years ago by ★ 1.4k • written 5.2 years ago by ▴ 80
0
votes
6
replies
2.5k
views
Removing Batch effect on the raw counts or normalised counts
DEseq2 batch effect RNAseq
updated 5.2 years ago by 42k • written 5.2 years ago by ▴ 30
1
vote
1
reply
1.0k
views
How to perform RNA-seq with such MDS plot?
limma batch effect rna-seq
updated 5.2 years ago by ★ 1.4k • written 5.2 years ago by • 0
5
votes
13
replies
3.1k
views
DESeq2 multiple group comparison (ANOVA) with batch effect
DESeq2 DEG ANOVA Batch effect Comparison
updated 5.2 years ago by 42k • written 5.2 years ago by • 0
0
votes
6
replies
1.2k
views
DESeq2: Error when correcting batch effect
deseq2 batch effect
updated 5.3 years ago by 42k • written 5.3 years ago by • 0
0
votes
4
replies
2.8k
views
deseq2 correction batch effect without design
deseq2 batch effect
updated 5.3 years ago by ★ 1.4k • written 5.3 years ago by • 0
8
votes
7
replies
2.2k
views
Confounded design, batch effect correction (edgeR)
rnaseq edger differential gene expression batch effect
updated 5.4 years ago by • 0 • written 6.2 years ago by ▴ 20
5
votes
3
replies
1.4k
views
Re-numbering blocking IDs on paired samples with duplicateCorrelation or design covariate
edger limma duplicateCorrelation batch effect
updated 5.4 years ago by ★ 28k • written 5.4 years ago by • 0
2
votes
8
replies
3.7k
views
removing batch effect using DESeq and sva
sva deseq2 batch effect PCA heatmap
updated 5.4 years ago by 42k • written 5.4 years ago by ▴ 10
10
votes
20
replies
21k
views
Batch Effect in DESeq2, how to control, how to remove it, how to address biological question
deseq2 batch effect batch
updated 5 weeks ago by 67k • written 5.5 years ago by ▴ 30
4
votes
4
replies
2.2k
views
Some questions for remove batch effect by using mnnCorrect
batch effect single cells mnnCorrect scran
updated 5.5 years ago by ★ 28k • written 5.5 years ago by ▴ 20
3
votes
12
replies
3.8k
views
ComBat normalization for batch effect change 0 values
ComBat batch effect sva normalization
updated 5.5 years ago by 67k • written 5.5 years ago by ▴ 10
0
votes
0
replies
880
views
removing confounding batch efffect with RUVg
RUVg RNAseq batch effect
5.7 years ago gtechbio ▴ 10
5
votes
1
reply
1.4k
views
Limma - Using removeBatchEffect before differential expression analysis
limma batch effect differential expression
updated 5.7 years ago by 67k • written 5.7 years ago by • 0
1
vote
1
reply
909
views
Handling batch effect with Limma
batch effect limma batch effect correction
updated 5.7 years ago by 51k • written 5.7 years ago by • 0
0
votes
4
replies
1.2k
views
Batch effect and edgeR analysis
batch effect edgeR RNA-seq
updated 5.7 years ago by 51k • written 5.7 years ago by ▴ 20
1
vote
2
replies
1.6k
views
WGCNA - confounding effect based on technical variables (some continuous)
WGCNA batch effect continuous
updated 5.7 years ago by ★ 3.0k • written 5.7 years ago by ▴ 20
7
votes
13
replies
2.2k
views
Taking into account strong batch effect in microarray differential expression analysis with limma
limma microarray hugeneST batch effect DE
updated 5.8 years ago by ★ 7.9k • written 5.8 years ago by ▴ 830
2
votes
2
replies
1.8k
views
Different DEG results using Ballgown and edgeR
edger ballgown rnaseq batch effect adjustvars
updated 5.8 years ago by 51k • written 5.8 years ago by • 0
1
vote
2
replies
1.1k
views
Aclaration of batch effect adjust in DE analysis
edger rnaseq batch effect
updated 5.8 years ago by 67k • written 5.8 years ago by • 0
0
votes
1
reply
859
views
DESeq2 modeling different organisms as batch effects
deseq2 batch effect across species
updated 5.9 years ago by 42k • written 5.9 years ago by • 0
0
votes
0
replies
870
views
Interpretation of PVCA result and what to correct for
pvca batch effect batch effect correction
6.0 years ago Sebastian Hesse ▴ 70
1
vote
4
replies
2.2k
views
model matrix for edgeR paired-design with batch effect
edgeR paired samples batch effect
updated 6.0 years ago by ★ 28k • written 6.0 years ago by • 0
2
votes
14
replies
2.3k
views
Differentiating between batch and treatment effects in edgeR, DESeq2
rnaseq batch effect deseq2 edger
updated 6.0 years ago by ★ 28k • written 6.0 years ago by ▴ 30
3
votes
2
replies
1.2k
views
Using deseq2 with batch effects and classification as downstream analysis
deseq2 batch effect classification
updated 6.1 years ago by 42k • written 6.1 years ago by • 0
0
votes
1
reply
1.2k
views
Normalization and Quality Control for Multiple scRNAseq Data Sets
normalization rnaseq genetics batch effect dropout
updated 6.1 years ago by ★ 13k • written 6.1 years ago by • 0
0
votes
0
replies
947
views
ComBat: missing peptide for one batch
batch effect missing value Combat
updated 6.1 years ago by 51k • written 6.1 years ago by • 0
3
votes
12
replies
5.5k
views
Batch correction when only some subjects have replicates across batches
limma batch effect rna-seq
updated 6.1 years ago by ★ 3.0k • written 6.1 years ago by ▴ 10
0
votes
2
replies
1.5k
views
RNA-seq unbalanced batch effect correction
rnaseq edger batch effect
updated 6.2 years ago by 67k • written 6.2 years ago by • 0
0
votes
2
replies
1.0k
views
Batch effect correction for class detection
batch effect unsupervised
updated 6.2 years ago by 67k • written 6.2 years ago by ▴ 20
2
votes
5
replies
4.5k
views
Batch Effect Correction
batch effect removebatcheffect edgeR rld DEseq2
6.3 years ago Antonio Ahn ▴ 10
3
votes
2
replies
9.0k
views
Problem with coefficients that are not estimable (limma)
limma batch effect
updated 3.5 years ago by • 0 • written 6.3 years ago by • 0
1
vote
4
replies
3.9k
views
Looking for Batch effects in PCA
batch effect pca
6.3 years ago • updated 21 months ago KB ▴ 50
1
vote
2
replies
2.7k
views
keep getting this error "number of rows is not the same across batches" even though my 2 matrices have the same row number
mnncorrect batch effect scran
updated 6.3 years ago by ★ 28k • written 6.3 years ago by • 0
2
votes
1
reply
989
views
Batch Variation-MDS Plot
edger R batch effect
updated 6.4 years ago by 51k • written 6.4 years ago by • 0
0
votes
0
replies
973
views
Help with multiple batch effects
combat sva batch effect
6.4 years ago Fp • 0
6
votes
12
replies
4.2k
views
Merging RNAseq Datasets of Different Depths
singlecellexperiment scran sequencing depth batch effect scrnaseq
updated 6.4 years ago by ★ 28k • written 6.4 years ago by • 0
0
votes
1
reply
1.1k
views
Model matrix not full rank
DESeq2 model matrix not full rank batch effect
updated 6.4 years ago by 42k • written 6.4 years ago by • 0
6
votes
7
replies
4.2k
views
Batch Correction with only one sample in a batch
batch effect deseq2 limma
updated 6.5 years ago by ★ 7.9k • written 6.5 years ago by ▴ 40
50 results • Page 1 of 1
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Replies
Comment: Differential Expression Analysis with unbalanced batches without replication bet by Thili • 0
Thank you for your reply. I currently have batch-corrected data processed with scvi-tools (specifically, totalvi) and have followed the sam…
Comment: Problem at champ.load by andrew.gibbons • 0
I'd love to know if anyone has a workaround too. I've tried rolling back ChAMP and R to the previous versions that others have said work wi…
Comment: GOstats kegg analysis in wheat - help - none of the objects in the first column by GV Yoshikawa • 0
Thank you for the reply. I tried swapping columns before asking, it made no difference. head(keggframeData) path_id kegg…
Answer: Differential Expression Analysis with unbalanced batches without replication bet by Gordon Smyth 51k
> Is there an alternative model or approach in tools like edgeR, limma-voom, or DESeq2 or any other that can handle confounded batch effect…
Comment: BiomaRt Possible Ensembl SSL connectivity problems detected. by Adam • 0
I just found this workaround: httr::set_config(config(ssl_verifypeer = FALSE, ssl_verifyhost = FALSE)) at [this Stack Overflow link][…
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A: Up/Down Regulated GeneList from edgeR and R
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