Does a TCGA dataset need batch effect removal?

Question

[Zahra]

Hi all

I have downloaded the TCGA-COAD dataset by TCGAbiolinks. The data is the HTSeq count matrix. Does it need any batch effect removal?

Thanks for any help.

[Hamid Ghaedi]

You need to analyze the expression matrix to see if there is any batch effect present in your dataset. A PCA analysis would give you insights on that.