[BioC] calling SAM using siggenes package
Aedin
aedin.culhane at ucd.ie
Mon Nov 1 11:45:37 CET 2004
Dear Saran,
When you use scan("testdata.txt"), the data is not read in as a matrix. It
is read in as a vector.
Try class(data) or length(data) to see.
You will need to convert the vector into a matrix.
t.data<-matrix(scan("testdata.txt"), byrow=TRUE, ncol=6)
Alternative try using
t.data<-read.table("testdata.txt", row.names=1, header=T) # assuming
gene/array labels in first col and row
check this using dim(t.data) and class(t.data).
The number of col, ncol(data) should equal the length(cl).
Hope this helps,
Aedin
So in R I do scan data as follow:
> data<-scan("testdata.txt")
Then for cl argument, it is a vector containing the class labels
of the samples. In this case I set the cl as follows:
> cl<-c(0,0,0,1,1,1)
So I went ahead and execute sam as follows:
So I went ahead and execute sam as follows:
> samdata<-sam(data,cl)
Then I got the following error:
Error in data[, c(x,y)] : incorrect number of dimensions.
Any advice on this will be greatly appreciated.
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