Showing : combat • reset
4
votes
21
replies
12k
views
DESeq2 and ComBat
deseq2 combat
updated 9.0 years ago by ▴ 610 • written 9.0 years ago by ▴ 100
52
votes
20
replies
48k
views
Batch correction in DESeq2
rnaseq batch effect deseq2 combat removebatcheffect()
updated 8.6 years ago by • 0 • written 9.1 years ago by ▴ 110
20
votes
18
replies
5.4k
views
Using of limma moderated t-test with "corrected" expression matrix resulting from ComBat batch effect correction
limma batch effect ComBat differential gene expression
updated 9.3 years ago by ▴ 870 • written 9.3 years ago by ▴ 840
8
votes
18
replies
14k
views
Batch correction by using ComBat function in sva package
deseq2 combat Knownbatcheffect Tutorial
updated 3.9 years ago by • 0 • written 5.3 years ago by ▴ 10
4
votes
16
replies
6.1k
views
How should I compare two different RNA-seq datasets using DESeq2 or EgdeR?
deseq2 limma combat
updated 5.6 years ago by 43k • written 5.6 years ago by ▴ 10
3
votes
12
replies
4.1k
views
ComBat normalization for batch effect change 0 values
ComBat batch effect sva normalization
updated 5.8 years ago by 67k • written 5.8 years ago by ▴ 10
10
votes
10
replies
4.6k
views
Method for batch correction
combat sva limma
updated 8.8 years ago by ▴ 120 • written 8.8 years ago by ▴ 60
1
vote
9
replies
3.1k
views
Removing batch effects from microarray data based on only a subset of samples
limma removebatcheffect() ComBat microarray
7.0 years ago jaro.slamecka ▴ 140
1
vote
8
replies
1.8k
views
Error in running Combat function
sva ComBat
updated 4.0 years ago by ★ 4.0k • written 4.0 years ago by ▴ 10
5
votes
8
replies
3.3k
views
Combat and dds Object
DESeq2 combat
updated 24 months ago by ★ 4.6k • written 3.5 years ago by ▴ 50
0
votes
8
replies
2.6k
views
Combat in gene pattern error annotation
software error ComBat Gene Pattern
updated 7.1 years ago by • 0 • written 9.5 years ago by • 0
3
votes
8
replies
2.7k
views
What type of data normalization for multiple microarrays?
normalization microarray combat
updated 8.4 years ago by ▴ 30 • written 8.4 years ago by • 0
2
votes
7
replies
2.5k
views
ComBat Error: in solve.default(t(des) %*% des) : System is computationally singuar: ...
ComBat sva
9.6 years ago edammer • 0
7
votes
7
replies
9.3k
views
batch effect : comBat or blocking in limma ?
batch effect combat limma block
updated 9.3 years ago by ★ 7.9k • written 9.3 years ago by ▴ 70
0
votes
6
replies
2.0k
views
Combine RNAseq datasets vst + Combat
combat vst deseq2
8.3 years ago User34591 • 0
0
votes
6
replies
6.9k
views
ComBat with multiple batches
sva combat 450k
9.0 years ago ben.run974 • 0
7
votes
6
replies
2.2k
views
sva ComBat implementation for multiple sources of batch effects
sva combat batch-adjustment
updated 4.7 years ago by ▴ 870 • written 4.7 years ago by ▴ 10
2
votes
6
replies
4.4k
views
Combat for batch effects
combat
9.9 years ago zhouxiuqing • 0
0
votes
6
replies
2.1k
views
analysis of multiple batches and multiple treatment conditions in scRNA-seq
limma deseq2 edger scRNAseq combat
updated 5.5 years ago by ▴ 270 • written 5.5 years ago by ▴ 670
0
votes
6
replies
1.9k
views
Problem in analysing microarray data with ComBat
combat
updated 22 months ago by ▴ 870 • written 9.7 years ago by • 0
2
votes
5
replies
6.9k
views
RNA-Seq Batch correction negative values
rna-seq batch-effect combat scran sva
updated 7.3 years ago by ★ 28k • written 7.3 years ago by ▴ 20
2
votes
5
replies
3.4k
views
Running ComBat Without a Batch Argument to Correct for Continuous, Numeric Covariates
combat sva
updated 7.3 years ago by ▴ 870 • written 7.3 years ago by • 0
0
votes
5
replies
1.4k
views
Variable of interest in combat correction
sva combat
updated 4.2 years ago by 67k • written 4.2 years ago by ▴ 10
10
votes
4
replies
3.4k
views
Adjust for multiple batches using combat
combat sva limma
updated 7.9 years ago by ★ 28k • written 7.9 years ago by • 0
1
vote
4
replies
7.4k
views
At least one covariate is confounded with batch! Please remove confounded covariates and rerun ComBat
ComBat sva
3.3 years ago NewBioInfo ▴ 10
1
vote
4
replies
2.8k
views
ComBat Normalisation - data is integers and some floats, confused?!
combat rnaseq combatnormalisation jeffleek sva
updated 15 months ago by • 0 • written 3.9 years ago by • 0
0
votes
4
replies
7.0k
views
ComBat: Error non-conformable arguments
ComBat
updated 9.7 years ago by 67k • written 9.7 years ago by • 0
1
vote
4
replies
3.9k
views
SVA package - for removing batch effect after DESeq - error in ComBat
sva combat
9.6 years ago GFM ▴ 20
0
votes
4
replies
1.7k
views
Reproducibility of results with ComBat
sva combat
updated 9.4 years ago by ▴ 650 • written 9.4 years ago by • 0
8
votes
4
replies
4.6k
views
correcting the batch effects in Limma and SVA
limma combat sva
updated 5.5 years ago by 52k • written 5.5 years ago by ▴ 670
3
votes
4
replies
5.2k
views
Running Combat in SVA with NA values in matrix
sva combat
9.1 years ago CC ▴ 10
0
votes
4
replies
938
views
Adjust RNA-seq counts (more than one batch variable) for plotting differentially expressed genes
ComBat sva edgeR
9 months ago Lucy ▴ 60
0
votes
4
replies
2.7k
views
DESeq2, outlier correction, Combat, NMF
deseq2 combat outliers NMF
updated 7.7 years ago by 43k • written 7.7 years ago by • 0
4
votes
4
replies
4.9k
views
sva::ComBat without covariate of interest?
sva combat
updated 10.2 years ago by ▴ 870 • written 10.2 years ago by ▴ 110
3
votes
4
replies
3.2k
views
How to normalize chromatin and RNA-Seq data together ?
atac-seq atac deseq2 sva combat
updated 7.9 years ago by 43k • written 7.9 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 5.4 years ago by ★ 1.4k • written 5.4 years ago by ▴ 80
7
votes
3
replies
3.5k
views
SVA: Including variable of interest in ComBat model matrix
combat sva SVA sva ComBat batch effect
updated 8.8 years ago by ▴ 870 • written 8.8 years ago by ▴ 20
2
votes
3
replies
1.7k
views
comBat/SVA with no "variable of interest" and two batches
combat sva covariates
updated 8.7 years ago by ▴ 420 • written 8.8 years ago by • 0
5
votes
3
replies
4.3k
views
about SVA: matrix of corrected expression values
SVA COMBAT
8.3 years ago Bogdan ▴ 670
1
vote
3
replies
7.0k
views
Combat - error - system is computationally singular
combat software error rnaseq complex-design
updated 10.3 years ago by ★ 3.0k • written 10.3 years ago by ▴ 20
0
votes
3
replies
1.2k
views
In SVA, the percent of biological variable of interest didnot change after adding SV1
SVA combat r microarray covariates
updated 5.2 years ago by 25k • written 5.2 years ago by • 0
0
votes
3
replies
1.4k
views
Extracting a subset of samples following SVA
Combat SVA Limma
updated 4.3 years ago by ★ 4.0k • written 4.3 years ago by • 0
5
votes
2
replies
7.7k
views
ComBat to remove batch effects from RNA Seq data
combat rnaseq
updated 8.3 years ago by ▴ 70 • written 8.3 years ago by ▴ 30
1
vote
2
replies
2.2k
views
Evaluation of diagnostic plot resulted from ComBat function regarding batch effect correction of a merged microarray dataset
ComBat diagnostic plot batch effect affymetrix microarrays sva
updated 9.0 years ago by ▴ 870 • written 9.0 years ago by ▴ 840
0
votes
2
replies
5.9k
views
Combat in R (SVA package) error message
combat software error
updated 9.7 years ago by ★ 3.0k • written 9.7 years ago by • 0
1
vote
2
replies
1.2k
views
Validity of duplicateCorrelation after ComBat in this scenario
limma ComBat SVA
updated 5.0 years ago by 52k • written 5.0 years ago by • 0
0
votes
2
replies
1.4k
views
Analyzing a RNA-Seq dataset with paired samples and 2 batches
deseq2 sva combat
updated 5.4 years ago by 43k • written 5.4 years ago by • 0
5
votes
2
replies
3.4k
views
ComBat - Including variable of interest in model matrix?
combat sva
updated 10.2 years ago by ▴ 650 • written 10.2 years ago by ▴ 10
2
votes
2
replies
1.6k
views
Modelling a multiplicative batch effect with DESeq2
deseq2 batch-effects ComBat
updated 5.3 years ago by 43k • written 5.3 years ago by ▴ 10
2
votes
2
replies
3.8k
views
ComBat: should the variable of interest be included into model matrix
ComBat
updated 10.2 years ago by ▴ 870 • written 10.2 years ago by ▴ 10
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Answer: Issues with seqlevelsStyle when making custom txdb objects for genomes/annotatio by Robert Castelo ★ 3.4k
Following the discussion of this post, the package [gDNAx](https://bioconductor.org/packages/gDNAx) has been fixed in devel and release 1.4…
Answer: Selection of correct coefficients or contrasts in DESeq2 by James W. MacDonald 67k
Using R's model formulation for three-way interactions is probably not the way to go here. Or at least I wouldn't do it that way. An easier…
Comment: How to generate circular cnetplot and color nodes and edges in the same plot ? by Blandine • 0
Thank you so much ! It's working !
Comment: how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K? by James W. MacDonald 67k
Yes. If you have the Illumina IDs, then all the annotation data that `cpg.annotate` uses will be based on hg19. It doesn't matter if TCGA l…
Comment: Recount3 data correspond to TCGA data by Leonardo Collado Torres ★ 1.1k
Thanks @fep29! ^^
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Comment: Recount3 data correspond to TCGA data
Answer: DESeq2- merging technical vs biological replicates
Answer: SingleCellExperiment convenience function for metadata+expression?
How to correct for tumor purity using DESeq2 to analyze TCGA tumor sample expression.
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