TCGA array expression and rnaseq expression batch correction

Question

[Omics data mining]

Hi everyone

In one of the article mentioned " Before starting the PDAC data analysis we first checked for possible batch effect in different types of data using Mbatch ". (Mishra et al 2019) here different data types refers to methylation, expression.

2) I found another script where batch effect have been explained in context to GEO and TCGA data. https://github.com/ELELAB/TCGAbiolinks_examples/blob/master/integration_script/case3_121019_integration.R

In my case, downloaded methylation ,expression (array) and expression (rnaseq). I have queries in context to -) Shall I perform batch correction of expression (array) data and expression (rnaseq) as represents the cross platform entities and if yes how ? Mbatch or TCGAbiolinks are suitable for this?

-) Preprocessing (missing data) should be done before the batch correction or after?

I new in batch correction area of analysis. I will appreciate all the suggestions.

Thanks

[Kevin Blighe]

What are you trying to do, ultimately?