Gene expression meta analysis

Question

[druggable]

Hi,

I am analyzing independent RNA-Seq datasets and doing a meta analysis. Is it valid to compare global transcription profiles from multiple datasets based on the fold changes? For each RNA-Seq dataset, I normalize counts within each dataset and then calculate the fold changes of all genes relative to the control. Now, I aim to create a heatmap of all the datasets based on the fold changes.

Thank you very much.

[egeulgen]

see this related question