Questions tagged [sva]

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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 ...
0
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0answers
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Model matrix design for limma-voom and batch effect correction

I've posted it on Bioconductor but didn't get a response, so I thought maybe I could get some help here (most likely the same audience but I'll try) I have multiple clusters in a 270 leukaemia sample ...
0
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2answers
79 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 ...
2
votes
1answer
87 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 ...
2
votes
1answer
430 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 ...