[BioC] Error when using spacialLayout in package arrayMagic

[Andreas Buness]

Hi Irene,

if you use the following lines it should work.

x <- read.delim(file="lc7b048rex2.DAT", skip=8, header=FALSE)
xHeader<- scan(file="lc7b048rex2.DAT", nlines=1, what="character", sep="\t")
colnames(x) <- xHeader
library(arrayMagic)
bg1<- spatialLayout(value=x$CH1B, row=x$ROW, col=x$COL, block=x$GRID)
plot.imageMatrix(bg1)

Your subsetting operation xx<-x[8:9223,]  does have a different effect; 
e.g. try:
str(xx)

Nevertheless I have not been aware that I always used already processed 
ScanAlyze files,
such that the example in arrayMagic does not work with the original data 
files. I will
clarify this.

Best Regards
Andreas

Irene Li wrote:
> 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
> 
> 
> Married. http://lifeevents.msn.com/category.aspx?cid=married
> 
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