The ImmGen V2 datasets was generated using a different set of amplification reagents (Ambion WT Expression Kit, not the Affymetrix GeneChip WT cDNA Synthesis and Amplification Kits).
Both V1 and V2 ImmGen datasets use the same Affymetrix Array (Affymetrix Mouse Gene 1.0 ST Array).
V1 and V2 results are very similar but do show some differences, and can NOT properly be compared or normalized to one another using standard normalization. V1 and V2 datasets have some overlapped cell types.