Open kvn95ss opened 5 months ago
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.
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 -![MDS_before_correction](https://github.com/zhangyuqing/ComBat-seq/assets/32951653/e7f798c0-7bff-4fbc-b7ac-1791710dfa6a)
And here's the after![MDS_after_correction](https://github.com/zhangyuqing/ComBat-seq/assets/32951653/34fab8b3-20d8-4836-af4a-0452173b4db1)
What could cause this? I tried separating the biotypes first then performing the batch correction, but the outcome was pretty much the same.