Dear list and LIMMA users,

I know this question is very often asked but I did not find the answer 
on the archives (and Limma user's guide, page 47).
My experimental design is built as following :
I have five replicates (human donors called 4 to 8 ) whom cells from 
blood were extracted and the same cells are treated (called DC) or not 
(called SC) for 4 hours and 18 hours.
So, we can consider samples are paired.

I only want the differential expressed genes between control and treated 
cells at 4 hours and 18 hours.

Here is my code :

>  Treatment
  [1] DC DC DC DC DC SC SC SC SC SC DC DC DC DC DC SC SC SC SC SC
Levels: DC SC
>  Time=factor(Targets$Time,level=c("4","18"))
>  Time
  [1] 4  4  4  4  4  4  4  4  4  4  18 18 18 18 18 18 18 18 18 18
Levels: 4 18
>  Donor=factor(Targets[,4])
>  Donor
  [1] 4 5 6 7 8 4 5 6 7 8 4 5 6 7 8 4 5 6 7 8
Levels: 4 5 6 7 8
>  design=model.matrix(~0+Treatment*Time+Donor)
>  design
  

>  design
    TreatmentDC TreatmentSC Time18 Donor5 Donor6 Donor7 Donor8 TreatmentSC:Time18
1            1           0      0      0      0      0      0                  0
2            1           0      0      1      0      0      0                  0
3            1           0      0      0      1      0      0                  0
4            1           0      0      0      0      1      0                  0
5            1           0      0      0      0      0      1                  0
6            0           1      0      0      0      0      0                  0
7            0           1      0      1      0      0      0                  0
8            0           1      0      0      1      0      0                  0
9            0           1      0      0      0      1      0                  0
10           0           1      0      0      0      0      1                  0
11           1           0      1      0      0      0      0                  0
12           1           0      1      1      0      0      0                  0
13           1           0      1      0      1      0      0                  0
14           1           0      1      0      0      1      0                  0
15           1           0      1      0      0      0      1                  0
16           0           1      1      0      0      0      0                  1
17           0           1      1      1      0      0      0                  1
18           0           1      1      0      1      0      0                  1
19           0           1      1      0      0      1      0                  1
20           0           1      1      0      0      0      1                  1
attr(,"assign")
[1] 1 1 2 3 3 3 3 4
attr(,"contrasts")
attr(,"contrasts")$Treatment
[1] "contr.treatment"

attr(,"contrasts")$Time
[1] "contr.treatment"

attr(,"contrasts")$Donor
[1] "contr.treatment"


>  fitDCSIGN = lmFit(DCSIGNsel,design)
>  fit_2<- eBayes(fitDCSIGN)
>  topTABLE=topTable(fit_2,number=10000)
>  head(topTABLE)


  

TreatmentDC 	TreatmentSC 	Time18 	Donor5 	Donor6 	Donor7 	Donor8 
TreatmentSC.Time18 	AveExpr 	F 	P.Value 	adj.P.Val
18,0039565 	18,0893776 	-0,06921285 	0,14003761 	0,00751388 
-0,17959668 	-0,39518169 	-0,05774869 	17,9121781 	9084,80254 
3,28E-35 	4,64E-31
17,6764306 	17,6523265 	0,10861812 	0,08220318 	-0,0058706 
-0,12147117 	-0,08119136 	0,04533621 	17,7047557 	8639,31256 	5,55E-35 
4,64E-31
17,5451093 	17,4890185 	0,03333055 	0,06786226 	-0,03553932 
-0,07273565 	-0,13275773 	0,08237079 	17,5196878 	8586,73092 	5,92E-35 
4,64E-31
17,5984155 	17,5441874 	0,10250253 	0,01347935 	-0,07462801 
-0,35432923 	-0,26347048 	-0,06969421 	17,4693395 	7910,39319 
1,39E-34 	8,20E-31
17,665938 	17,51601 	0,12567687 	0,10254981 	0,0012268 	-0,39209921 
-0,44094147 	0,13771659 	17,5423888 	7711,69463 	1,82E-34 	8,42E-31
17,4376721 	17,5047189 	0,06959671 	0,07916199 	-0,08220435 
0,01004729 	0,01116857 	-0,06673615 	17,4929445 	7589,67631 	2,15E-34 
8,42E-31
17,3227449 	17,3110054 	0,05350864 	0,07092431 	0,01562233 
-0,11608052 	-0,22506562 	0,03662242 	17,3018652 	7460,38367 	2,57E-34 
8,63E-31


So, I don't understand the colnames and why I did not obtain log fold 
change ?

Is my design correct ?

Many thans for your reply !!!

Ingrid



-- 
Ingrid MERCIER
Mycobacterial Interactions with Host Cells Team
Institute of Pharmacology&  Structural Biology
CNRS
BP 64182
F-31077 Toulouse Cedex France
Tel +33 (0)5 61 17 54 63




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