Questions tagged [sva]

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Surrogate variable analysis for paired RNA seq experiment

I have an RNAseq experiment with 1000s of samples. Each sample comes from a patient and was treated either with a drug or DMSO (as control). I am currently deciding between SVA and RUVseq to account ...
nhaus's user avatar
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1 vote
1 answer
136 views

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 ...
Kento's user avatar
  • 67
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1 answer
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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 ...
Umair Khan's user avatar
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2 answers
4k views

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 ...
Mohammad's user avatar
3 votes
1 answer
198 views

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 ...
Kent's user avatar
  • 105
3 votes
1 answer
1k views

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 ...
Nikita Vlasenko's user avatar