Showing : Batch effect • reset
3
votes
7
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6.7k
views
limma::removeBatchEffect into DESeq2
deseq2 limma batch effect
updated 4.7 years ago by ★ 4.0k • written 4.7 years ago by • 0
4
votes
5
replies
3.8k
views
How to incorporate batch effect that is only present in one level into the design?
linear model batch effect DESeq2 design
updated 4.7 years ago by 68k • written 4.7 years ago by • 0
2
votes
8
replies
5.5k
views
Remove batch effect limma, "Coefficients not estimable" warning and design matrix
limma deseq2 batch design batch effect
4.7 years ago Pietro ▴ 40
2
votes
2
replies
1.3k
views
edgeR batch effect correction for unevenly distributed groups
rnaseq edgeR batch effect
updated 4.7 years ago by 52k • written 4.7 years ago by • 0
2
votes
5
replies
4.4k
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 5.0 years ago by ★ 13k • written 5.0 years ago by ▴ 840
0
votes
0
replies
833
views
Concatenating different runs from the same pool of barcoded CyTOF samples
batch effect cytof
5.1 years ago mikhael.manurung ▴ 280
0
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10
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3.6k
views
DEseq2 design formula correcting for batch
deseq2 design formula batch effect
updated 5.2 years ago by ★ 1.4k • written 5.2 years ago by • 0
0
votes
1
reply
1.2k
views
problem for interpretation of resulted ComBat() plot
ComBat sva batch effect RNA-seq
updated 5.4 years ago by ▴ 870 • written 5.4 years ago by ▴ 10
1
vote
4
replies
2.2k
views
edgeR design matrix for 2 variables + batch effect
egdeR design matrix batch effect
updated 5.4 years ago by 52k • written 5.4 years ago by • 0
3
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2
replies
2.5k
views
Variation between technical replicates (DESeq2, batch effects)
rnaseq deseq2 differential expression batch effect replicates
updated 5.6 years ago by 43k • written 5.6 years ago by ▴ 10
1
vote
2
replies
1.2k
views
The order used in common practce? batch effect removel and normalization
normalization batch effect
updated 5.6 years ago by ▴ 420 • written 5.6 years ago by ▴ 10
2
votes
3
replies
1.4k
views
Design for introducing batch effect in DESeq2
deseq2 combat batch effect rna-seq edger
updated 5.7 years ago by ★ 1.4k • written 5.7 years ago by ▴ 80
0
votes
6
replies
3.1k
views
Removing Batch effect on the raw counts or normalised counts
DEseq2 batch effect RNAseq
updated 5.7 years ago by 43k • written 5.7 years ago by ▴ 30
1
vote
1
reply
1.2k
views
How to perform RNA-seq with such MDS plot?
limma batch effect rna-seq
updated 5.7 years ago by ★ 1.4k • written 5.7 years ago by • 0
5
votes
13
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3.6k
views
DESeq2 multiple group comparison (ANOVA) with batch effect
DESeq2 DEG ANOVA Batch effect Comparison
updated 5.7 years ago by 43k • written 5.7 years ago by • 0
0
votes
6
replies
1.4k
views
DESeq2: Error when correcting batch effect
deseq2 batch effect
updated 5.8 years ago by 43k • written 5.8 years ago by • 0
0
votes
4
replies
3.3k
views
deseq2 correction batch effect without design
deseq2 batch effect
updated 5.8 years ago by ★ 1.4k • written 5.8 years ago by • 0
8
votes
7
replies
2.5k
views
Confounded design, batch effect correction (edgeR)
rnaseq edger differential gene expression batch effect
updated 5.8 years ago by • 0 • written 6.6 years ago by ▴ 20
5
votes
3
replies
1.5k
views
Re-numbering blocking IDs on paired samples with duplicateCorrelation or design covariate
edger limma duplicateCorrelation batch effect
updated 5.8 years ago by ★ 28k • written 5.8 years ago by • 0
2
votes
8
replies
4.1k
views
removing batch effect using DESeq and sva
sva deseq2 batch effect PCA heatmap
updated 5.9 years ago by 43k • written 5.9 years ago by ▴ 10
10
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20
replies
24k
views
Batch Effect in DESeq2, how to control, how to remove it, how to address biological question
deseq2 batch effect batch
updated 6 months ago by 68k • written 5.9 years ago by ▴ 30
5
votes
4
replies
2.5k
views
Some questions for remove batch effect by using mnnCorrect
batch effect single cells mnnCorrect scran
updated 6.0 years ago by ★ 28k • written 6.0 years ago by ▴ 20
3
votes
12
replies
4.5k
views
ComBat normalization for batch effect change 0 values
ComBat batch effect sva normalization
updated 6.0 years ago by 68k • written 6.0 years ago by ▴ 10
0
votes
0
replies
953
views
removing confounding batch efffect with RUVg
RUVg RNAseq batch effect
6.1 years ago gtechbio ▴ 10
5
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1
reply
1.6k
views
Limma - Using removeBatchEffect before differential expression analysis
limma batch effect differential expression
updated 6.1 years ago by 68k • written 6.1 years ago by • 0
1
vote
1
reply
991
views
Handling batch effect with Limma
batch effect limma batch effect correction
updated 6.1 years ago by 52k • written 6.1 years ago by • 0
0
votes
4
replies
1.3k
views
Batch effect and edgeR analysis
batch effect edgeR RNA-seq
updated 6.2 years ago by 52k • written 6.2 years ago by ▴ 20
1
vote
2
replies
1.9k
views
WGCNA - confounding effect based on technical variables (some continuous)
WGCNA batch effect continuous
updated 6.2 years ago by ★ 3.0k • written 6.2 years ago by ▴ 20
7
votes
13
replies
2.5k
views
Taking into account strong batch effect in microarray differential expression analysis with limma
limma microarray hugeneST batch effect DE
updated 6.3 years ago by ★ 7.9k • written 6.3 years ago by ▴ 840
2
votes
2
replies
2.0k
views
Different DEG results using Ballgown and edgeR
edger ballgown rnaseq batch effect adjustvars
updated 6.3 years ago by 52k • written 6.3 years ago by • 0
1
vote
2
replies
1.3k
views
Aclaration of batch effect adjust in DE analysis
edger rnaseq batch effect
updated 6.3 years ago by 68k • written 6.3 years ago by • 0
0
votes
1
reply
963
views
DESeq2 modeling different organisms as batch effects
deseq2 batch effect across species
updated 6.4 years ago by 43k • written 6.4 years ago by • 0
0
votes
0
replies
974
views
Interpretation of PVCA result and what to correct for
pvca batch effect batch effect correction
6.4 years ago Sebastian Hesse ▴ 70
1
vote
4
replies
2.5k
views
model matrix for edgeR paired-design with batch effect
edgeR paired samples batch effect
updated 6.5 years ago by ★ 28k • written 6.5 years ago by • 0
2
votes
14
replies
2.7k
views
Differentiating between batch and treatment effects in edgeR, DESeq2
rnaseq batch effect deseq2 edger
updated 6.5 years ago by ★ 28k • written 6.5 years ago by ▴ 30
3
votes
2
replies
1.4k
views
Using deseq2 with batch effects and classification as downstream analysis
deseq2 batch effect classification
updated 6.5 years ago by 43k • written 6.5 years ago by • 0
0
votes
1
reply
1.3k
views
Normalization and Quality Control for Multiple scRNAseq Data Sets
normalization rnaseq genetics batch effect dropout
updated 6.5 years ago by ★ 13k • written 6.5 years ago by • 0
0
votes
0
replies
1.0k
views
ComBat: missing peptide for one batch
batch effect missing value Combat
updated 6.6 years ago by 52k • written 6.6 years ago by • 0
3
votes
12
replies
6.7k
views
Batch correction when only some subjects have replicates across batches
limma batch effect rna-seq
updated 6.6 years ago by ★ 3.0k • written 6.6 years ago by ▴ 10
0
votes
2
replies
1.6k
views
RNA-seq unbalanced batch effect correction
rnaseq edger batch effect
updated 6.6 years ago by 68k • written 6.6 years ago by • 0
0
votes
2
replies
1.1k
views
Batch effect correction for class detection
batch effect unsupervised
updated 6.7 years ago by 68k • written 6.7 years ago by ▴ 20
2
votes
5
replies
5.0k
views
Batch Effect Correction
batch effect removebatcheffect edgeR rld DEseq2
6.7 years ago Antonio Ahn ▴ 10
3
votes
2
replies
10.0k
views
Problem with coefficients that are not estimable (limma)
limma batch effect
updated 3.9 years ago by • 0 • written 6.8 years ago by • 0
1
vote
4
replies
4.2k
views
Looking for Batch effects in PCA
batch effect pca
6.8 years ago • updated 2.3 years ago KB ▴ 50
1
vote
2
replies
3.2k
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 6.8 years ago by ★ 28k • written 6.8 years ago by • 0
2
votes
1
reply
1.1k
views
Batch Variation-MDS Plot
edger R batch effect
updated 6.8 years ago by 52k • written 6.8 years ago by • 0
0
votes
0
replies
1.1k
views
Help with multiple batch effects
combat sva batch effect
6.8 years ago Fp • 0
6
votes
12
replies
4.9k
views
Merging RNAseq Datasets of Different Depths
singlecellexperiment scran sequencing depth batch effect scrnaseq
updated 6.8 years ago by ★ 28k • written 6.8 years ago by • 0
0
votes
1
reply
1.2k
views
Model matrix not full rank
DESeq2 model matrix not full rank batch effect
updated 6.9 years ago by 43k • written 6.9 years ago by • 0
6
votes
7
replies
4.8k
views
Batch Correction with only one sample in a batch
batch effect deseq2 limma
updated 6.9 years ago by ★ 7.9k • written 6.9 years ago by ▴ 40
50 results • Page 1 of 1
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Comment: Differing results with DESeq2 by JKim • 0
My two cents. I think it would be more straightforward if you use cellmeans model. Have a look at [A guide to creating design matrices for …
Answer: CluserProfiler message "No gene can be mapped" by James W. MacDonald 68k
Your gene IDs are things like this: `Mpyr-NLJ1B.v3.hap1.scaffold1.g290550`, and the genes in your term2gene table are things like this: `Mp…
Answer: RNA-seq input to GRaNIE by James W. MacDonald 68k
This is [covered in the vignette.][1] [1]: https://bioconductor.org/packages/release/bioc/vignettes/GRaNIE/inst/doc/GRaNIE_packageDe…
Answer: Help using reduceSimMatrix with a custom annotation by sergisayolspuig ▴ 80
Hi there, `reduceSimMatrix()` expects a "GOALL" keytype in the OrgDb object when called with `children=TRUE` (which is the default for thi…
Answer: Analyzing TnSeq data with DESeq2 by cold.wolverine.arku • 0
That's a great use case of DESeq2! Even though it's not specifically tailored for TnSeq data, your approach to normalize and run explorator…
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A: Unbalanced experiment with multiple samples from each patient.
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Answer: ROAST for small sets
Answer: ROAST for small sets
A: conceptual question about FDR, FDR adjusted p-value and q-value
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