Hi, there,

I'm working on a time-course microarray analysis and got some problems.
The design is very simple. All the other time point samples were compared to
time 0 and the comparison between every two connected time points were also
made. So here is what I did:

> library(limma)
> targets=readTargets()
> spottypes=readSpotTypes()
> RG=read.maimages(targets, source="genepix")
> RG$genes$Status=controlStatus (spottypes, RG)
>RG=backgroundCorrect(RG, method="normexp", offset=50)
>MA=normalizeWithinArrays(RG, method="loess")
>MA=normalizeBetweenArrays(MA, method="quantile")
>MA2=MA[MA$genes$Status=="cDNA",]
>MAave = avereps (MA2, ID=MA2$genes$Name)

##### Then I separate the color channels so that I can make comparison
between any two time points###########

> targets2=targetsA2C(targets)
> targets2
     channel.col SlideNumber   FileName      Date Target
1.1            1           1  12h-R.gpr 3/19/2009   12hr
1.2            2           1  12h-R.gpr 3/19/2009    ref
2.1            1           2  R-12h.gpr 3/19/2009    ref
2.2            2           2  R-12h.gpr 3/19/2009   12hr
3.1            1           3   1D-R.gpr 3/24/2009   day1
3.2            2           3   1D-R.gpr 3/24/2009    ref
4.1            1           4   R-1D.gpr 3/24/2009    ref
4.2            2           4   R-1D.gpr 3/24/2009   day1
5.1            1           5   2D-R.gpr 3/24/2009   day2
5.2            2           5   2D-R.gpr 3/24/2009    ref
6.1            1           6   R-2D.gpr 3/24/2009    ref
6.2            2           6   R-2D.gpr 3/24/2009   day2
7.1            1           7   3D-R.gpr 3/26/2009   day3
7.2            2           7   3D-R.gpr 3/26/2009    ref
8.1            1           8   R-3D.gpr 3/26/2009    ref
8.2            2           8   R-3D.gpr 3/26/2009   day3
9.1            1           9   4D-R.gpr 3/26/2009   day4
9.2            2           9   4D-R.gpr 3/26/2009    ref
10.1           1          10   R-4D.gpr 3/26/2009    ref
10.2           2          10   R-4D.gpr 3/26/2009   day4
11.1           1          11   7D-R.gpr 3/31/2009   day7
11.2           2          11   7D-R.gpr 3/31/2009    ref
12.1           1          12   R-7D.gpr 3/31/2009    ref
12.2           2          12   R-7D.gpr 3/31/2009   day7
13.1           1          13  21D-R.gpr 3/31/2009  day21
13.2           2          13  21D-R.gpr 3/31/2009    ref
14.1           1          14  R-21D.gpr 3/31/2009    ref
14.2           2          14  R-21D.gpr 3/31/2009  day21
15.1           1          15 12h-1D.gpr  4/2/2009   12hr
15.2           2          15 12h-1D.gpr  4/2/2009   day1
16.1           1          16 1D-12h.gpr  4/2/2009   day1
16.2           2          16 1D-12h.gpr  4/2/2009   12hr
17.1           1          17  1D-2D.gpr  4/2/2009   day1
17.2           2          17  1D-2D.gpr  4/2/2009   day2
18.1           1          18  2D-1D.gpr  4/2/2009   day2
18.2           2          18  2D-1D.gpr  4/2/2009   day1
19.1           1          19  2D-3D.gpr 4/14/2009   day2
19.2           2          19  2D-3D.gpr 4/14/2009   day3
20.1           1          20  3D-2D.gpr 4/14/2009   day3
20.2           2          20  3D-2D.gpr 4/14/2009   day2
21.1           1          21  3D-4D.gpr 4/14/2009   day3
21.2           2          21  3D-4D.gpr 4/14/2009   day4
22.1           1          22  4D-3D.gpr 4/14/2009   day4
22.2           2          22  4D-3D.gpr 4/14/2009   day3
23.1           1          23  4D-7D.gpr 4/16/2009   day4
23.2           2          23  4D-7D.gpr 4/16/2009   day7
24.1           1          24  7D-4D.gpr 4/16/2009   day7
24.2           2          24  7D-4D.gpr 4/16/2009   day4
25.1           1          25 7D-21D.gpr 4/16/2009   day7
25.2           2          25 7D-21D.gpr 4/16/2009  day21
26.1           1          26 21D-7D.gpr 4/16/2009  day21
26.2           2          26 21D-7D.gpr 4/16/2009   day7

> u=unique(targets2$Target)
> lev=c("12hr","ref","day1","day2","day3","day4","day7","day21")
> f=factor(targets2$Target, levels=lev)
> design=model.matrix(~0+f)
> design
   f12hr fref fday1 fday2 fday3 fday4 fday7 fday21
1      1    0     0     0     0     0     0      0
2      0    1     0     0     0     0     0      0
3      0    1     0     0     0     0     0      0
4      1    0     0     0     0     0     0      0
5      0    0     1     0     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     1     0     0     0     0      0
9      0    0     0     1     0     0     0      0
10     0    1     0     0     0     0     0      0
11     0    1     0     0     0     0     0      0
12     0    0     0     1     0     0     0      0
13     0    0     0     0     1     0     0      0
14     0    1     0     0     0     0     0      0
15     0    1     0     0     0     0     0      0
16     0    0     0     0     1     0     0      0
17     0    0     0     0     0     1     0      0
18     0    1     0     0     0     0     0      0
19     0    1     0     0     0     0     0      0
20     0    0     0     0     0     1     0      0
21     0    0     0     0     0     0     1      0
22     0    1     0     0     0     0     0      0
23     0    1     0     0     0     0     0      0
24     0    0     0     0     0     0     1      0
25     0    0     0     0     0     0     0      1
26     0    1     0     0     0     0     0      0
27     0    1     0     0     0     0     0      0
28     0    0     0     0     0     0     0      1
29     1    0     0     0     0     0     0      0
30     0    0     1     0     0     0     0      0
31     0    0     1     0     0     0     0      0
32     1    0     0     0     0     0     0      0
33     0    0     1     0     0     0     0      0
34     0    0     0     1     0     0     0      0
35     0    0     0     1     0     0     0      0
36     0    0     1     0     0     0     0      0
37     0    0     0     1     0     0     0      0
38     0    0     0     0     1     0     0      0
39     0    0     0     0     1     0     0      0
40     0    0     0     1     0     0     0      0
41     0    0     0     0     1     0     0      0
42     0    0     0     0     0     1     0      0
43     0    0     0     0     0     1     0      0
44     0    0     0     0     1     0     0      0
45     0    0     0     0     0     1     0      0
46     0    0     0     0     0     0     1      0
47     0    0     0     0     0     0     1      0
48     0    0     0     0     0     1     0      0
49     0    0     0     0     0     0     1      0
50     0    0     0     0     0     0     0      1
51     0    0     0     0     0     0     0      1
52     0    0     0     0     0     0     1      0

> colnames(design)=lev
> fit=lmFit(MAave, design)
Error in lm.fit(design, t(M)) : incompatible dimensions

Does anyone know what is wrong with this? Thanks.

Wei


-- 
Wei Xu
Aquatic Animal Health Laboratory
Pathobiology and Diagnostic Investigation
College of Veterinary Medicine
Michigan State University
East Lansing, MI, 48824
Tel: 1-517-432-8258

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