Comparing gene expression data between datasets

Question

[kpukacz]

Hello Everyone,

I am currently working on examining how the expression rates of certain algal genes change under different conditions, using existing RNA-seq data from the Short Reads Archive (SRA). Naturally, most DGE and similar methods such as DESeq2 are specifically designed to work on data from a single experiment, however, is there any way to normalise data to minimise the differences in expression rates between samples, which can then be used for a PCA analysis?

Thanks in advance,

Krz.