RNA sequencing data and batch effect
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4 months ago

Hi. We have performed two batches of RNA sequencing with different piplines and thus, generated two different count matrix. Besides, one is hg38 and the other is hg19. My first question is if I can performed batch correction using ComBat function (or combat-seq) from sva since different upstream pipeline and different reference genome was used. The second question is if there is any other methods to correct the batch effect for such a condition. Btw, there were some samples that were sequenced in both two batches of RNA seq. I dont know if this clue can provide any hints.

RNA-Seq Batch combat Effect • 223 views
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What is the background of this? Just run the same pipeline for both and same genome if that is the only difference here. Makes no sense to process them differently, does it?

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