Hello ! 

I have four data-sets. These data-sets are from different studies and or cell strains.

Two of them do only have a control and a treated vector.

I was following the default approach for the meta-analysis for rna-seq : 

https://cran.r-project.org/web/packages/metaRNASeq/vignettes/metaRNASeq.pdf

I understand that i have to perform the same filtering/approach on all data-sets in order to compare them properly. In order to do this it is essential to have uniform data-sets. This is most likely not the case for two of the data-sets so i will  have to find a way to make them uniform.

In the tutorial HTSFilter is used , but it can not be performed on data-sets with no replicates. My problem is that i really want to use all the data-sets.

What is the ( most likely ) best way to get to do this ?

I am very grateful for any help !