Samples M708_pos_8wk.CEL M728_pos_7.5wk.CEL M729_pos_12wk.CEL M739_neg_14wk.CEL M739_pos_14wk.CEL M753_neg_8.5wk.CEL M753_pos_8.5wk.CEL Normalistation and expression analysis Done with Partek GS 6.6 using RMA algorithm PCA Partek GS Differential expression pvalues with limma in R FDR Qvalues calculated with QVALUE Contrasts: A - 5 positive versus 2 negative samples B - 2 positive (M739 and M753) versus 2 negative paired samples (M739 and M753) C - gene expression change between the 5 positive samples (they represent 5 different developmental stages, so I'm interested in changes with development. The order of the samples is: 1st: M728 (7.5 weeks), 2nd: M708 (8 weeks), 3rd: M753 (8.5 weeks), 4th: M729 (12 weeks), 5th M739 (14 weeks). As such, I am not sure (and probably won't be before we see the data) whether to pair the first 3 and compare with the last 2, or whether to compare between the 5 individual samples. X_vs_Y where X = M728Pos, M708Pos and M753 pos Y = M729pos and M739pos