normalize between 2 different platform

Question

[Edalat]

I have some Non-coding RNAseq data with 2 different platform,Illumina Genome Analyzer IIx and Illumina HiSeq 2000,I want to do meta analysis and before that I should normalize them,how should I normalize between 2 different platform?

[Asaf]

I think that the library preparation is more critical than the sequencing machine. If the preparation was different, since each method has its biases, the comparison is not valid.

[Edalat]

thank you for a replay.you mean I should investigate their library preparation ?

[Asaf]

Yes, exactly. If they're public it's more problematic.