Showing : Batch effect • reset
3
votes
7
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5.1k
views
limma::removeBatchEffect into DESeq2
deseq2 limma batch effect
updated 3.7 years ago by ★ 3.9k • written 3.7 years ago by • 0
4
votes
5
replies
2.9k
views
How to incorporate batch effect that is only present in one level into the design?
linear model batch effect DESeq2 design
updated 3.8 years ago by 66k • written 3.8 years ago by • 0
2
votes
8
replies
4.3k
views
Remove batch effect limma, "Coefficients not estimable" warning and design matrix
limma deseq2 batch design batch effect
3.8 years ago Pietro ▴ 40
2
votes
2
replies
985
views
edgeR batch effect correction for unevenly distributed groups
rnaseq edgeR batch effect
updated 3.8 years ago by 50k • written 3.8 years ago by • 0
2
votes
5
replies
3.3k
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 4.1 years ago by ★ 13k • written 4.1 years ago by ▴ 830
0
votes
0
replies
643
views
Concatenating different runs from the same pool of barcoded CyTOF samples
batch effect cytof
4.2 years ago mikhael.manurung ▴ 280
0
votes
10
replies
2.5k
views
DEseq2 design formula correcting for batch
deseq2 design formula batch effect
updated 4.3 years ago by ★ 1.4k • written 4.3 years ago by • 0
0
votes
1
reply
912
views
problem for interpretation of resulted ComBat() plot
ComBat sva batch effect RNA-seq
updated 4.5 years ago by ▴ 850 • written 4.5 years ago by ▴ 10
1
vote
4
replies
1.6k
views
edgeR design matrix for 2 variables + batch effect
egdeR design matrix batch effect
updated 4.5 years ago by 50k • written 4.5 years ago by • 0
3
votes
2
replies
1.8k
views
Variation between technical replicates (DESeq2, batch effects)
rnaseq deseq2 differential expression batch effect replicates
updated 4.7 years ago by 42k • written 4.7 years ago by ▴ 10
1
vote
2
replies
922
views
The order used in common practce? batch effect removel and normalization
normalization batch effect
updated 4.7 years ago by ▴ 420 • written 4.7 years ago by ▴ 10
2
votes
3
replies
1.1k
views
Design for introducing batch effect in DESeq2
deseq2 combat batch effect rna-seq edger
updated 4.7 years ago by ★ 1.4k • written 4.7 years ago by ▴ 80
0
votes
6
replies
2.0k
views
Removing Batch effect on the raw counts or normalised counts
DEseq2 batch effect RNAseq
updated 4.8 years ago by 42k • written 4.8 years ago by ▴ 30
1
vote
1
reply
880
views
How to perform RNA-seq with such MDS plot?
limma batch effect rna-seq
updated 4.8 years ago by ★ 1.4k • written 4.8 years ago by • 0
5
votes
13
replies
2.8k
views
DESeq2 multiple group comparison (ANOVA) with batch effect
DESeq2 DEG ANOVA Batch effect Comparison
updated 4.8 years ago by 42k • written 4.8 years ago by • 0
0
votes
6
replies
1.1k
views
DESeq2: Error when correcting batch effect
deseq2 batch effect
updated 4.8 years ago by 42k • written 4.8 years ago by • 0
0
votes
4
replies
2.4k
views
deseq2 correction batch effect without design
deseq2 batch effect
updated 4.9 years ago by ★ 1.4k • written 4.9 years ago by • 0
8
votes
7
replies
1.9k
views
Confounded design, batch effect correction (edgeR)
rnaseq edger differential gene expression batch effect
updated 4.9 years ago by • 0 • written 5.7 years ago by ▴ 20
5
votes
3
replies
1.2k
views
Re-numbering blocking IDs on paired samples with duplicateCorrelation or design covariate
edger limma duplicateCorrelation batch effect
updated 4.9 years ago by ★ 28k • written 4.9 years ago by • 0
2
votes
8
replies
3.4k
views
removing batch effect using DESeq and sva
sva deseq2 batch effect PCA heatmap
updated 5.0 years ago by 42k • written 5.0 years ago by ▴ 10
10
votes
18
replies
17k
views
Batch Effect in DESeq2, how to control, how to remove it, how to address biological question
deseq2 batch effect batch
5.0 years ago Mozart ▴ 30
4
votes
4
replies
1.8k
views
Some questions for remove batch effect by using mnnCorrect
batch effect single cells mnnCorrect scran
updated 5.1 years ago by ★ 28k • written 5.1 years ago by ▴ 20
3
votes
12
replies
3.3k
views
ComBat normalization for batch effect change 0 values
ComBat batch effect sva normalization
updated 5.1 years ago by 66k • written 5.1 years ago by ▴ 10
0
votes
0
replies
783
views
removing confounding batch efffect with RUVg
RUVg RNAseq batch effect
5.2 years ago gtechbio ▴ 10
5
votes
1
reply
1.3k
views
Limma - Using removeBatchEffect before differential expression analysis
limma batch effect differential expression
updated 5.2 years ago by 66k • written 5.2 years ago by • 0
1
vote
1
reply
796
views
Handling batch effect with Limma
batch effect limma batch effect correction
updated 5.2 years ago by 50k • written 5.2 years ago by • 0
0
votes
4
replies
1.0k
views
Batch effect and edgeR analysis
batch effect edgeR RNA-seq
updated 5.2 years ago by 50k • written 5.2 years ago by ▴ 10
1
vote
2
replies
1.4k
views
WGCNA - confounding effect based on technical variables (some continuous)
WGCNA batch effect continuous
updated 5.3 years ago by ★ 3.0k • written 5.3 years ago by ▴ 20
7
votes
13
replies
1.9k
views
Taking into account strong batch effect in microarray differential expression analysis with limma
limma microarray hugeneST batch effect DE
updated 5.3 years ago by ★ 7.9k • written 5.3 years ago by ▴ 830
2
votes
2
replies
1.6k
views
Different DEG results using Ballgown and edgeR
edger ballgown rnaseq batch effect adjustvars
updated 5.4 years ago by 50k • written 5.4 years ago by • 0
1
vote
2
replies
1.0k
views
Aclaration of batch effect adjust in DE analysis
edger rnaseq batch effect
updated 5.4 years ago by 66k • written 5.4 years ago by • 0
0
votes
1
reply
752
views
DESeq2 modeling different organisms as batch effects
deseq2 batch effect across species
updated 5.4 years ago by 42k • written 5.4 years ago by • 0
0
votes
0
replies
758
views
Interpretation of PVCA result and what to correct for
pvca batch effect batch effect correction
5.5 years ago Sebastian Hesse ▴ 70
1
vote
4
replies
2.0k
views
model matrix for edgeR paired-design with batch effect
edgeR paired samples batch effect
updated 5.6 years ago by ★ 28k • written 5.6 years ago by • 0
2
votes
14
replies
1.9k
views
Differentiating between batch and treatment effects in edgeR, DESeq2
rnaseq batch effect deseq2 edger
updated 5.6 years ago by ★ 28k • written 5.6 years ago by ▴ 20
3
votes
2
replies
1.1k
views
Using deseq2 with batch effects and classification as downstream analysis
deseq2 batch effect classification
updated 5.6 years ago by 42k • written 5.6 years ago by • 0
0
votes
1
reply
1.1k
views
Normalization and Quality Control for Multiple scRNAseq Data Sets
normalization rnaseq genetics batch effect dropout
updated 5.6 years ago by ★ 13k • written 5.6 years ago by • 0
0
votes
0
replies
820
views
ComBat: missing peptide for one batch
batch effect missing value Combat
updated 5.7 years ago by 50k • written 5.7 years ago by • 0
3
votes
12
replies
4.8k
views
Batch correction when only some subjects have replicates across batches
limma batch effect rna-seq
updated 5.7 years ago by ★ 3.0k • written 5.7 years ago by ▴ 10
0
votes
2
replies
1.4k
views
RNA-seq unbalanced batch effect correction
rnaseq edger batch effect
updated 5.7 years ago by 66k • written 5.7 years ago by • 0
0
votes
2
replies
901
views
Batch effect correction for class detection
batch effect unsupervised
updated 5.8 years ago by 66k • written 5.8 years ago by ▴ 20
2
votes
5
replies
4.2k
views
Batch Effect Correction
batch effect removebatcheffect edgeR rld DEseq2
5.8 years ago Antonio Ahn ▴ 10
3
votes
2
replies
7.9k
views
Problem with coefficients that are not estimable (limma)
limma batch effect
updated 3.0 years ago by • 0 • written 5.9 years ago by • 0
1
vote
4
replies
3.5k
views
Looking for Batch effects in PCA
batch effect pca
5.9 years ago • updated 16 months ago KB ▴ 50
1
vote
2
replies
2.3k
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 5.9 years ago by ★ 28k • written 5.9 years ago by • 0
2
votes
1
reply
904
views
Batch Variation-MDS Plot
edger R batch effect
updated 5.9 years ago by 50k • written 5.9 years ago by • 0
0
votes
0
replies
832
views
Help with multiple batch effects
combat sva batch effect
5.9 years ago Fp • 0
6
votes
12
replies
3.7k
views
Merging RNAseq Datasets of Different Depths
singlecellexperiment scran sequencing depth batch effect scrnaseq
updated 5.9 years ago by ★ 28k • written 5.9 years ago by • 0
0
votes
1
reply
975
views
Model matrix not full rank
DESeq2 model matrix not full rank batch effect
updated 5.9 years ago by 42k • written 5.9 years ago by • 0
6
votes
7
replies
3.7k
views
Batch Correction with only one sample in a batch
batch effect deseq2 limma
updated 6.0 years ago by ★ 7.9k • written 6.0 years ago by ▴ 40
50 results • Page 1 of 1
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Comment: Why is longestConsecutive() depreceated in version 2.72 (BioC version 3.19)? by ATpoint ★ 4.2k
I don't have an answer to the "why" but maybe a simple reimplemention will do: ```r seqs <- c("ATCATCGTATCAAAGTC", "AAAACGTATCAAAGTC", "TG…
Comment: How to add Ensembl ids after Pseudobulk analysis by DESeq2 by Guido Hooiveld ★ 4.0k
After checking `?DESeqDataSetFromMatrix` note this information: arguments provided to SummarizedExperiment including rowRanges and met…
Answer: Error in gseDO function by Guido Hooiveld ★ 4.0k
Yes, you are missing something. :-) For a GSEA you will need to use as input all genes that you are analyzing; these genes should be ran…
Comment: GSVA function by Robert Castelo ★ 3.3k
No, negative values may occur after log transformation when the `log(x)` is taken from a positive number `x with 0 < x < 1`, and therefore …
Comment: conumee with Infinium MethylationEPIC v2.0 by sgomez • 0
Hi Max, Could you try this? https://support.bioconductor.org/p/9136138/#9136840
Votes
A: Comparison between two different group's pathway analysis results
DiffBind Batch Effect
A: DiffBind Batch Effect
A: DiffBind Batch Effect
C: DiffBind Batch Effect
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