Showing : sva • reset
0
votes
3
replies
288
views
A ComBat-seq issue: the covariates are confounded
ComBat-seq sva
updated 4 weeks ago by ▴ 850 • written 5 weeks ago by • 0
3
votes
6
replies
308
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Surrogate variable analysis for paired RNA seq experiment
RUVSeq sva
5 weeks ago nhaus ▴ 30
0
votes
2
replies
185
views
pca with VST of DESeq2 give 100% variance in PC1
DESeq2 sva
6 weeks ago michelafrancesconi8 • 0
0
votes
4
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448
views
Adjust RNA-seq counts (more than one batch variable) for plotting differentially expressed genes
ComBat sva edgeR
6 weeks ago Lucy ▴ 60
0
votes
8
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456
views
DESeq and SVA for batch effect
DESeq2 BatchEffect sva
10 weeks ago michelafrancesconi8 • 0
0
votes
3
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320
views
Would I treat surrogate variables as batches?
DESeq2 sva
updated 10 weeks ago by 65k • written 11 weeks ago by ▴ 10
0
votes
5
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610
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Can SVs identified from sva be used for removeBatchEffect() in DESeq2
sva DESeq2 BatchEffect limma
updated 4 months ago by ★ 4.1k • written 4 months ago by • 0
0
votes
1
reply
400
views
DESeq2 interaction term + sva
sva DESeq2
updated 4 months ago by 42k • written 5 months ago by ▴ 20
0
votes
2
replies
356
views
combat output NaN
sva
6 months ago maxixian1990 • 0
0
votes
4
replies
633
views
How to correct for known and surrogate variables in DESeq2?
DESeq2 BatchEffect sva limma
updated 4 weeks ago by 42k • written 6 months ago by • 0
5
votes
2
replies
799
views
ComBat_seq function in sva package does not return a matrix
sva ComBat ComBat-seq Bioconductor ComBat_seq
7 months ago Federico ▴ 10
5
votes
9
replies
1.3k
views
Batch correction and repeated measures
RUVSeq sva limma
updated 4 weeks ago by 50k • written 7 months ago by ▴ 10
0
votes
1
reply
481
views
SVA for MatrixeQTL - which "variable of interest"?
matrixeqtl sva
updated 8 months ago by 65k • written 8 months ago by • 0
2
votes
3
replies
1.1k
views
bulk RNA-seq analysis using R : batch effect : One question concerning Combat-seq and one question concerning DESeq2 design = batch + condition
BatchEffect sva DESeq2 RNASeqData limma
updated 9 months ago by 65k • written 9 months ago by ▴ 10
0
votes
2
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651
views
Fluidigm Data Batch Correction
sva limma
updated 10 months ago by 50k • written 10 months ago by • 0
3
votes
3
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986
views
how to remove batch effects of RNA seq data based on continuous variables(like surrogate variables from sva package) using combatseq or limma (remove…
combatseq RNASeqData sva limma
10 months ago amnahsiddiqa ▴ 10
2
votes
3
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1.2k
views
PCA for QC should include subset of top variable genes or full set of genes in RNAseq data?
BatchQC RNASeqData sva BatchEffect
updated 10 months ago by ★ 4.1k • written 10 months ago by ▴ 10
0
votes
0
replies
404
views
How to go for Batch correction in RNA-seq expeiment conducted based on imbalanced Experimental design ?
RNASeqData BatchEffect sva
10 months ago amnahsiddiqa ▴ 10
1
vote
4
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2.0k
views
ComBat Normalisation - data is integers and some floats, confused?!
combat rnaseq combatnormalisation jeffleek sva
updated 7 months ago by • 0 • written 3.2 years ago by • 0
19 results • Page 1 of 1
Recent ...
Replies
Comment: all variables in design formula must be columns in colData (Deseq2) error by Galina • 0
thank you!
Comment: all variables in design formula must be columns in colData (Deseq2) error by ATpoint ★ 4.1k
coldata_rat <- data.frame(conditions=..., batch=...)
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it by robersy • 0
Thank you all for your comments. I will follow your suggestions.
Comment: Numerical differences in DESeq2 output depending on different design matrix cons by Ken C • 0
Hi Michael, thanks a lot for your prompt reply! Not sure if this is appropriate or if you are the right person to ask -- is there anything…
Comment: Numerical differences in DESeq2 output depending on different design matrix cons by Ken C • 0
Well, if I look at genes with baseMean>50, then the relative absolute difference in log2FoldChange (say over the absolute log2FoldChange of…
Votes
biomaRt not working - lazy table error
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Comment: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Comment: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
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