[BioC] errors in imageplot() in limma

[michael watson (IAH-C)]

Hi

I am getting some rather confusing messages from the imageplot() function in limma.  As in my previous mail, I am using a version of Bioconductor 1.2 from the website from about 2 weeks ago.

I am reading the data in from a GenePix file but I want to use Medians rather than Means, so I did:

>RG <- read.maimages("F:\\IBDV_Experiment\\same_layout\\lame#9.adjusted.gpr",columns=list(Rf = "F635.Median",Gf = "F532.Median", Rb = "B635.Median", Gb = "B532.Median"))

This seemed to work.  Then:

>MA <- MA.RG(RG)

Again, this seemed to work fine.  Then I did:

>> imageplot(MA, layout=list(ngrid.r=8,ngrid.c=4,nspot.r=16,nspot.c=16))

And got the error:

Error in imageplot(MA, layout = list(ngrid.r = 8, ngrid.c = 4, nspot.r = 16,  : 
        Number of image spots does not agree with layout dimensions

Now the layout I have given it is 8*4*16*16 = 8192

So I checked:

> length(MA$M)
[1] 8192
> length(MA$A)
[1] 8192

Hmmmmm.... so that is why I am confused, because the number of image spots DOES agree with the layout dimensions....

Any help would be greatly appreciated :-D

Thanks
Mick