[BioC] Qspline (again)

[Paul Boutros]

Hi all,

Perhaps these questions are the result of a profound misunderstanding of
the object-model at use here, or even R itself.  I'm struggling to get the
above method (normalize.qspline, in module Affy) to work.

This is the procedure I have followed:
> data <-read.table("data.txt");
> data2 <- data.matrix(data);
> targetav <- c(2335.958, 1932.225);
> test <- normalize.qspline(data2, target=targetav, samples=100,
verbose=TRUE);

The error message I get is:
Error in rep(data, t1) : invalid number of copies in "rep"

I don't see the function rep() being called in normalize.qspline at all.
Any ideas what's going on here?  A few records from data (the frame) look
like:
         qry1.S635 qry1.S532
H3001A10     613.0     602.5
H3001A12    1208.5    1019.0
H3001B01     337.0     353.0
H3001C02     495.0     497.5

And a few records from data2 (the data.matrix) would look like:
         qry1.S635 qry1.S532
H3001A10     613.0     602.5
H3001A12    1208.5    1019.0
H3001B01     337.0     353.0
H3001C02     495.0     497.5

i.e. identical to my eyes.

Any help or ideas or anything very much appreciated! :)
Paul