Possible to directly compare RNA-Seq and DGE data?

Question

[ez935]

Hello,

I have sequencing data from RNA-Seq and DGE (Digital Gene Expression) for the following conditions:

RNA-Seq: Condition A + Condition B

DGE: Condition B + Condition C

Would it be possible to compare Condition A against Condition C from different methods? These experiments were done at different times so we no longer have the samples available to run them on the same platform.

Thanks!

[WouterDeCoster]

To add to Sean Davis : No, library prep/quantification methods will seriously bias the result. You would be doing a technical comparison of the method RNA-seq with the method DGE, and not the underlying biological comparison of condition A vs condition C.

Answer 1

[Sean Davis]

Unfortunately, probably not.