RE: "Where does the multiplicity of libraries come in?   Generally any of the procedure that generate statistics require a single input data set which is why I am confused about the mention of all those libraries."   The experiment is as follows: Four treament groups- Fresh Pollen, Fresh Supplement, Old Pollen, Old Supplement Each treatment group had 11 cages of bees (50 newly emerged bees per cage) Within each treatment group we disected four tissues (hypo glands, mouth parts, ileum and rectum) from 3 individuals per cage and pooled together for sequencing. For each of the cages we monitored mortality, thorax developemnt and hypo gland development.   What I am interested in is the tissue as a whole. So how do the bacterial reads (abundance), reguardless of treatment, correlate to the mortality, thorax developemnt and hypo gland development and once a significant correlation is found, how do I determine shared variance?       ... View more