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
imageplot, and limma generally, assumes that your expression data is
in
standard order. This means that ngrid.r, ngrid.c, nspot.r, nspot.c are
in
that order as slowest to fastest moving indices. If your data is not
in
that order, you have to re-order it.
You an re-order data to change the dimension orders using a judicious
usage
of the dim and aperm functions, but this is not part of limma.
Gordon
At 12:31 PM 16/03/2004, Anna Cao wrote:
>Hi All,
>
>I$B!G(Bm 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 $B"*(B 30
>31 32$B!D(B.. 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
