[BioC] limma makeContrasts

[Lorenzo Bomba]

Dear all,

I have a conceptual problem with the "makeContrast"  function in Limma:
doing  a factorial design and the follow are the  targetfile and the design matrix

targetfile

FileName	Scrofa	Treatment
S10M	S127	DR
S11	S52	DR
S12	S304	DR
S13	S9	NODR
S14	S52	DR
S15	S304	DR
S17rt	S304	DR
S18	S66	DR
S19	S66	NODR
S20	S304	NODR
S21	S93	NODR
S22	S93	NODR


> design
   S127.DR S304.DR S304.NODR S52.DR S66.DR S66.NODR S9.NODR S93.NODR
1        1       0         0      0      0        0       0        0
2        0       0         0      1      0        0       0        0
3        0       1         0      0      0        0       0        0
4        0       0         0      0      0        0       1        0
5        0       0         0      1      0        0       0        0
6        0       1         0      0      0        0       0        0
7        0       1         0      0      0        0       0        0
8        0       0         0      0      1        0       0        0
9        0       0         0      0      0        1       0        0
10       0       0         1      0      0        0       0        0
11       0       0         0      0      0        0       0        1
12       0       0         0      0      0        0       0        1
attr(,"assign")
[1] 1 1 1 1 1 1 1 1
attr(,"contrasts")
attr(,"contrasts")$TS
[1] "contr.treatment"

I want see the difference between the NODR and the DR group taking in account that they belong to different mothers ( S127   S304  .....etc ). How can I set the makeContrast....
I tried  in this two ways.... but I don't know the difference between the first and the second

1)cont.matrix <- makeContrasts( DRvsNODR=(S127.DR+S304.DR+S52.DR)-(S304.NODR+S66.NODR+S9.NODR+S93.NODR), levels=design)

2) cont.matrix <- makeContrasts( DRvsNODR=(S127.DR-S304.DR-S52.DR)-(S304.NODR-S66.NODR-S9.NODR-S93.NODR), levels=design)

Could you help me please???

Thanks in advance!

Lorenzo