Questions tagged [sva]
The sva tag has no usage guidance.
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Can I Incorporate svaseq() into GSEA/GSVA analysis?
I understand GSEA/GSVA can take microarray-like expression matrix such as the output of voom() or vst(). However, I have a question on how we can also use svaseq() variables, correct the output from ...
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Error in apply(dat[, batch == batch_level], 1, function(x) { : dim(X) must have a positive length
I am new here so forgive me if I don't provide all the details in the first go. There is a very similar question (how to solve “dim(X) must have a positive length” at running ComBat function in R) but ...
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how to solve “dim(X) must have a positive length” at running ComBat function in R
I used ComBat() for batch effect correction in my expression data. basically, that function inputs are expression data, Batch covariate, and Model matrix for the ...
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sva for RNA-Seq data without known phenotype
I have been working on RNA-Seq data from two different cohorts, and they show very strong batch effect (~35% variance explained by 1st component in PCA). Since I am trying to do a class discovery from ...
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How to get the corrected matrix after SVA batch effect correction
I ran SVA to remove batch effects for my bulk RNAseq experiments, but now I need to somehow correct my data matrix in order to ...
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