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I'm working with smallRNA data and performed batch control with Combat_Seq (bioconductor version).
I used the below command -
library('sva') corrected_batch <- ComBat_seq(as.matrix(counts), batch = coldata$Small_Seq_Batch) corrected_batch <- as.data.frame(corrected_batch)
Here's a MDS plot before correcting -
And here's the after
What could cause this? I tried separating the biotypes first then performing the batch correction, but the outcome was pretty much the same.
The text was updated successfully, but these errors were encountered:
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I'm working with smallRNA data and performed batch control with Combat_Seq (bioconductor version).
I used the below command -
Here's a MDS plot before correcting -
And here's the after
What could cause this? I tried separating the biotypes first then performing the batch correction, but the outcome was pretty much the same.
The text was updated successfully, but these errors were encountered: