[BioC] RE: Dye Swap Experiments

[Gordon Smyth]

At 11:32 PM 20/06/2003, michael watson (IAH-C) wrote:
>Hi Gordon
>
>I'm still playing with limma and just came across another oddity you may 
>or may not be aware of!
>
>In the help for imageplot(), your example is this:
>
>M <- rnorm(8*4*16*16)
>imageplot(M,layout=list(ngrid.r=8,ngrid.c=4,nspot.r=16,nspot.c=16))
>
>Here we see that the array consists of 8 rows of sub-grids and 4 columns.
>
>However, if I execute this command, i get a plot with 4 rows of subgrids 
>and 8 columns...?

I deliberately chose to plot arrays on their side, i.e., the "top" of the 
array is on the left of the screen. That is why the help document says that 
the first spot on the array is on the bottom left of the plot. I choose to 
do this because most computer screens are wider than high.

>Also, is there way of generating the matrix of data easily from say a 
>GenePix file?
>I find this difficult as GenePix just has a single co-ordinate for a 
>sub-grid called
>"Block" and there is nothing in the actual file to say how many rows and 
>columns there are.

Do you mean generate the layout parameters? If you have a GenePix 
allocation list (gal) file in your working directory with extension ".gal", 
then you can type

gal <- readGAL()
layout <- getLayout(gal)

to extract the layout parameters.

>However, even with user input, it would be good to be able to convert from 
>a list to a matrix
>
>Thanks
>Mick

Gordon