[BioC] limma imageplot

[Anna Cao]

Hi All,

I’m using the imageplot function in limma to look for spatial artifacts on
the array. I used oligo arrays with a grid dimension of 5(x-axis) x
12(y-axis) and spot dimension of 30 (x-axis) x 9 (y-axis). I use layout =
ngrid.r=5,ngrid.c=12,nspot.r=30,nspot.c=9. My genes in the raw file are
listed in the order from 1 --> 16200 and the order is shown below:

Actual Spot dimension alignment (30 x 9 so that each piece of grid has 270
spots):
1 2 3 4 5 6 7 8 9 → 30
31 32….. and so on

But the imageplot shows the spot dimension in the order below (a sample
grid):
9 18.............270th spot
8 17
7 16
6 15
5 14
4 13
3 12
2 11
1 10.............261th spot

As for the Grid dimension (5x12 so that there's 60 grid total):
The original grid dimension alignment is:
01 02 03 04 05
06 07 08 09 10
11
16
21
26
............60th grid

The image plot shows grid dimension in the order below:
12 24.......60th grid
11 23
10 22
9  21
8  20
7  19
6  18
5  17
4  16
3  15
2  14
1  13........49th grid

Is there anyway I can change the dimension order so it fits the actual spot
and grid alignment?

Thanks,

Anna