Dear Panagiotis,

I've preformed diff.exp. analysis for the Lexgen samples.
The metaseqr (EdgeR) results are at:
http://genomics-lab.fleming.gr/fleming/GKlab/run268/metaseqr_Hum_vs_Sal2/index.html

I'd suggest you take all expresstions at
http://genomics-lab.fleming.gr/fleming/GKlab/run268/metaseqr_Hum_vs_Sal2/lists/metaseqr_all_out_HUM_vs_SAL.txt.gz
and make a scatterplot against the array results.

I've also run cufflinks/diff, results at:
http://genomics-lab.fleming.gr/fleming/GKlab/run268/cuffdiff_Hum_vs_Sal

BW,
Martin