Analysis of the effect of gender and compartment by principal component analysis (PCA). RNA from the 25 pigs (3 types of cells, 2 time points) were hybridized with the new Snowball Affymetrix microarray. 140 microarrays out of the 150 were analysed using the Partek Software (10 microarrays did not pass quality check). (A) PCA was done on the gender of the pigs (50 males - blue, 100 females - red). No specific cluster could be observed. (B) PCA was also applied to the array data from the different compartments harvested (AM in red, BMDM in blue and MDM in green) and the treatment (sphere for 0 h and cube for 7 h LPS). Both compartment and time point can be clustered. Macrophages stimulated with LPS (boxes) are separated from the controls (spheres). AM (red) form a separate cluster whereas BMDM (blue) and MDM (green) are grouped together.