[BioC] limma imageplot

[Gordon Smyth]

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