# [BioC] Doubt to set layout in limma

Marcelo Luiz de Laia mlaia at fcav.unesp.br
Thu May 6 19:38:25 CEST 2004

```Hi All,

I have a idiots doubt!

I have a data files with R and G intensities.

The layout in the slides is:

1     2     3    . . . 23
3 1 4 3 1 4 3 1 4
A 2 X 3 2 X 3 2 X 3
1 4 2 1 4 2 1 4 2
3 1 4 3 1 4 3 1 4
B 2 X 3 2 X 3 2 X 3
1 4 2 1 4 2 1 4 2
.
.
.
N

The data file is:

Row Col Grid Dup label  Gf Gb  CV Rf Rb DV
A   1   3    1   A-1:3 198 74 124 47 29 18
A   1   1    1   A-1:1 180 69 111 31 29  1
A   1   4    1   A-1:4  63 55   7 30 29  1
A   1   2    1   A-1:2  73 68   6 29 29  0
A   1   3    2   A-1:3 151 63  89 41 28 13
A   1   1    2   A-1:1  89 62  28 31 28  3
A   1   4    2   A-1:4  72 66   6 31 30  1
A   1   2    2   A-1:2  66 58   9 34 27  7
A   1   B    B   A-1:B  61 65   0 28 28  0
A   2   3    1   A-2:3 122 56  65 34 30  3
A   2   1    1   A-2:1  74 57  17 30 28  2
A   2   4    1   A-2:4  74 57  17 29 28  1
A   2   2    1   A-2:2 275 61 214 43 30 13
A   2   3    2   A-2:3 109 64  45 33 31  2
A   2   1    2   A-2:1 102 62  40 31 28  3
A   2   4    2   A-2:4  93 62  31 31 28  3
A   2   2    2   A-2:2 347 62 284 34 30  4
A   2   B    B   A-2:B  60 62   0 30 30  0

B=blank

I have ngrid.r=3, ngrid.c=3, nspot.r=14, nspot.c=23, ndups=2, spacing=4, start="topleft".

limma will duplicate spot each four spacing. But, when it found a "B", what it to do? Because blank spot dont have dup. How do I do to solve this problem? Or it dont have solution.

--
Marcelo Luiz de Laia, M.Sc.
Dep. de Tecnologia, Lab. Bioquímica e de Biologia Molecular