[BioC] Error when using spacialLayout in package arrayMagic

[Irene Li]

Hi,

I’ve just started learning Bioconductor. I downloaded the data 
lc7b048rex2.DAT from http://llmpp.nih.gov/lymphoma/ . When I tried to view 
the special homogenueity of hybridization, this was the error I’ve got:
>x=read.delim(“lc7b048rex2.DAT”) bg1<- spatialLayout(value=x$CH1B, 
>row=x$ROW, col=x$COL, block=x$GRID)
Error in if (totalNumberOfValues%%(max(col) * nrOfBlocksPerRow) != 0) { :
        missing value where TRUE/FALSE needed

Then I got rid of the text information in the first 7 rows
>xx<-x[8:9223,]
>bg2<- spatialLayout(value=xx$CH1B, row=xx$ROW, col=xx$COL, block=xx$GRID)
Warning messages:
1: "-" not meaningful for factors in: Ops.factor(block, 1)
2: "-" not meaningful for factors in: Ops.factor(block, 1)

I had the same error massage even when I specified nrOfBlocksPerRow as 1 or 
8 instead of the default value of 4. Every tuple of bg2 now has a value of 
“NA”. Of course, I cannot plot bg2 using plot.imageMatrix(…).

How can I get the spatial layout of the background?

Any help is greatly appreciated.

Many thanks.

Irene


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