1. PA14_OD1, vs CF5_OD1   c(17,22),c(21,26)
2. PA14_OD1, vs C3719_OD1 c(11,16)
3. PA14_OD1, vs PACS2_OD1 c(8,27)

4. MTB_OD1, vs CF5_OD1 c(7,12)
5. MTB_OD1, vs C3719_OD1
6. MTB_OD1, vs PACS2_OD1

7. B133_OD1 vs CF5_OD1 c(13,30)
8. B133_OD1 vs C3719_OD1
9. B133_OD1 vs PACS2_OD1

The consensus list of 1-9 gene lists (each containing only the genes that are diff. expressed with a corrected P value of <0.05)

10. PA14_OD3, vs CF5_OD3 c(10,15), c(14,19)
11. PA14_OD3, vs C3719_OD3 c(9,28)
12. PA14_OD3, vs PACS2_OD3 c(20,25)

13. MTB_OD3, vs CF5_OD3 c(24,29),
14. MTB_OD3, vs C3719_OD3
15. MTB_OD3, vs PACS2_OD3


16. B133_OD3 vs CF5_OD3 c(18,23),
17. B133_OD3 vs C3719_OD3
18. B133_OD3 vs PACS2_OD3

The consensus list of 10-18 gene lists (each containing only the genes that are diff. expressed with a corrected P value of <0.05)

# pipeline:
Rscript diff-exp-deseq3.r
for i in de*csv
do
 awk -f get-padj-le0.05.awk $i >> $i"2"
done