Showing : batch effect • reset
3
votes
7
replies
6.2k
views
limma::removeBatchEffect into DESeq2
deseq2 limma batch effect
updated 4.3 years ago by ★ 4.0k • written 4.3 years ago by • 0
4
votes
5
replies
3.5k
views
How to incorporate batch effect that is only present in one level into the design?
linear model batch effect DESeq2 design
updated 4.3 years ago by 67k • written 4.3 years ago by • 0
2
votes
8
replies
5.1k
views
Remove batch effect limma, "Coefficients not estimable" warning and design matrix
limma deseq2 batch design batch effect
4.3 years ago Pietro ▴ 40
2
votes
2
replies
1.1k
views
edgeR batch effect correction for unevenly distributed groups
rnaseq edgeR batch effect
updated 4.4 years ago by 52k • written 4.4 years ago by • 0
2
votes
5
replies
3.9k
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 4.7 years ago by ★ 13k • written 4.7 years ago by ▴ 840
0
votes
0
replies
772
views
Concatenating different runs from the same pool of barcoded CyTOF samples
batch effect cytof
4.8 years ago mikhael.manurung ▴ 280
0
votes
10
replies
3.1k
views
DEseq2 design formula correcting for batch
deseq2 design formula batch effect
updated 4.9 years ago by ★ 1.4k • written 4.9 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 5.0 years ago by ▴ 870 • written 5.0 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 5.1 years ago by 52k • written 5.1 years ago by • 0
3
votes
2
replies
2.2k
views
Variation between technical replicates (DESeq2, batch effects)
rnaseq deseq2 differential expression batch effect replicates
updated 5.2 years ago by 43k • written 5.3 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 5.3 years ago by ▴ 420 • written 5.3 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 5.3 years ago by ★ 1.4k • written 5.3 years ago by ▴ 80
0
votes
6
replies
2.7k
views
Removing Batch effect on the raw counts or normalised counts
DEseq2 batch effect RNAseq
updated 5.3 years ago by 43k • written 5.3 years ago by ▴ 30
1
vote
1
reply
1.1k
views
How to perform RNA-seq with such MDS plot?
limma batch effect rna-seq
updated 5.3 years ago by ★ 1.4k • written 5.3 years ago by • 0
5
votes
13
replies
3.2k
views
DESeq2 multiple group comparison (ANOVA) with batch effect
DESeq2 DEG ANOVA Batch effect Comparison
updated 5.3 years ago by 43k • written 5.3 years ago by • 0
0
votes
6
replies
1.2k
views
DESeq2: Error when correcting batch effect
deseq2 batch effect
updated 5.4 years ago by 43k • written 5.4 years ago by • 0
0
votes
4
replies
2.9k
views
deseq2 correction batch effect without design
deseq2 batch effect
updated 5.4 years ago by ★ 1.4k • written 5.4 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 5.5 years ago by • 0 • written 6.3 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 5.5 years ago by ★ 28k • written 5.5 years ago by • 0
2
votes
8
replies
3.8k
views
removing batch effect using DESeq and sva
sva deseq2 batch effect PCA heatmap
updated 5.5 years ago by 43k • written 5.5 years ago by ▴ 10
10
votes
20
replies
22k
views
Batch Effect in DESeq2, how to control, how to remove it, how to address biological question
deseq2 batch effect batch
updated 11 weeks ago by 67k • written 5.6 years ago by ▴ 30
5
votes
4
replies
2.3k
views
Some questions for remove batch effect by using mnnCorrect
batch effect single cells mnnCorrect scran
updated 5.6 years ago by ★ 28k • written 5.7 years ago by ▴ 20
3
votes
12
replies
4.0k
views
ComBat normalization for batch effect change 0 values
ComBat batch effect sva normalization
updated 5.7 years ago by 67k • written 5.7 years ago by ▴ 10
0
votes
0
replies
897
views
removing confounding batch efffect with RUVg
RUVg RNAseq batch effect
5.8 years ago gtechbio ▴ 10
5
votes
1
reply
1.5k
views
Limma - Using removeBatchEffect before differential expression analysis
limma batch effect differential expression
updated 5.8 years ago by 67k • written 5.8 years ago by • 0
1
vote
1
reply
924
views
Handling batch effect with Limma
batch effect limma batch effect correction
updated 5.8 years ago by 52k • written 5.8 years ago by • 0
0
votes
4
replies
1.2k
views
Batch effect and edgeR analysis
batch effect edgeR RNA-seq
updated 5.8 years ago by 52k • written 5.8 years ago by ▴ 20
1
vote
2
replies
1.7k
views
WGCNA - confounding effect based on technical variables (some continuous)
WGCNA batch effect continuous
updated 5.9 years ago by ★ 3.0k • written 5.9 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 5.9 years ago by ★ 7.9k • written 5.9 years ago by ▴ 840
2
votes
2
replies
1.8k
views
Different DEG results using Ballgown and edgeR
edger ballgown rnaseq batch effect adjustvars
updated 5.9 years ago by 52k • written 5.9 years ago by • 0
1
vote
2
replies
1.1k
views
Aclaration of batch effect adjust in DE analysis
edger rnaseq batch effect
updated 5.9 years ago by 67k • written 5.9 years ago by • 0
0
votes
1
reply
871
views
DESeq2 modeling different organisms as batch effects
deseq2 batch effect across species
updated 6.0 years ago by 43k • written 6.0 years ago by • 0
0
votes
0
replies
899
views
Interpretation of PVCA result and what to correct for
pvca batch effect batch effect correction
6.1 years ago Sebastian Hesse ▴ 70
1
vote
4
replies
2.3k
views
model matrix for edgeR paired-design with batch effect
edgeR paired samples batch effect
updated 6.2 years ago by ★ 28k • written 6.2 years ago by • 0
2
votes
14
replies
2.4k
views
Differentiating between batch and treatment effects in edgeR, DESeq2
rnaseq batch effect deseq2 edger
updated 6.2 years ago by ★ 28k • written 6.2 years ago by ▴ 30
3
votes
2
replies
1.3k
views
Using deseq2 with batch effects and classification as downstream analysis
deseq2 batch effect classification
updated 6.2 years ago by 43k • written 6.2 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 6.2 years ago by ★ 13k • written 6.2 years ago by • 0
0
votes
0
replies
967
views
ComBat: missing peptide for one batch
batch effect missing value Combat
updated 6.2 years ago by 52k • written 6.2 years ago by • 0
3
votes
12
replies
5.7k
views
Batch correction when only some subjects have replicates across batches
limma batch effect rna-seq
updated 6.2 years ago by ★ 3.0k • written 6.2 years ago by ▴ 10
0
votes
2
replies
1.5k
views
RNA-seq unbalanced batch effect correction
rnaseq edger batch effect
updated 6.3 years ago by 67k • written 6.3 years ago by • 0
0
votes
2
replies
1.0k
views
Batch effect correction for class detection
batch effect unsupervised
updated 6.3 years ago by 67k • written 6.3 years ago by ▴ 20
2
votes
5
replies
4.6k
views
Batch Effect Correction
batch effect removebatcheffect edgeR rld DEseq2
6.4 years ago Antonio Ahn ▴ 10
3
votes
2
replies
9.2k
views
Problem with coefficients that are not estimable (limma)
limma batch effect
updated 3.6 years ago by • 0 • written 6.4 years ago by • 0
1
vote
4
replies
3.9k
views
Looking for Batch effects in PCA
batch effect pca
6.4 years ago • updated 23 months ago KB ▴ 50
1
vote
2
replies
2.8k
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 6.4 years ago by ★ 28k • written 6.4 years ago by • 0
2
votes
1
reply
1.0k
views
Batch Variation-MDS Plot
edger R batch effect
updated 6.5 years ago by 52k • written 6.5 years ago by • 0
0
votes
0
replies
1000
views
Help with multiple batch effects
combat sva batch effect
6.5 years ago Fp • 0
6
votes
12
replies
4.3k
views
Merging RNAseq Datasets of Different Depths
singlecellexperiment scran sequencing depth batch effect scrnaseq
updated 6.5 years ago by ★ 28k • written 6.5 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 6.5 years ago by 43k • written 6.5 years ago by • 0
6
votes
7
replies
4.3k
views
Batch Correction with only one sample in a batch
batch effect deseq2 limma
updated 6.6 years ago by ★ 7.9k • written 6.6 years ago by ▴ 40
50 results • Page 1 of 1
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Answer: Cross-validation with multiple control subgroups in limma by Gordon Smyth 52k
limma doesn't do cross-validation or resampling. Like most classical linear modeling procedures in statistics, limma uses a statistical mod…
Comment: Issues with seqlevelsStyle when making custom txdb objects for genomes/annotatio by Robert Castelo ★ 3.4k
Hi Hervé, thank you very much for your input into how to properly build and manage TxDb objects. gDNAx has two main inputs, one or more BAM…
Comment: Biostrings: Error writing long reads (>200 kbps) with writeQualityScaledXStringS by Aidan ▴ 60
Quick update: this is fixed in a branch awaiting PR to Biostrings (https://github.com/Bioconductor/Biostrings/pull/122). Should be in `deve…
Answer: Can DESeq2's design compensate for sequencing experimental design shortcomings? by Michael Love 43k
For statistical analysis plans, I recommend working with a local statistician or someone familiar with linear models in R. I have to reserv…
Comment: how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K? by xiaofeiwang198266 • 0
Thanks for your reply!
Votes
C: edgeR and lack of counts ID on CPM matrix
A: DESeq2 Following RSEM
A: importing RSEM data into DESeq2
A: Expected counts from RSEM in DESeq2
A: Using RSEM reads for DESeq2
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