[BioC] normalize.quantiles generating incorrect output

[Jeffrey Chang]

Hello everybody,

I'm using the normalize.quantiles function from the "affy" package 
version 1.3.27, using R 1.8.1 on Mac OS X.  I'm seeing some unexpected 
behavior when I try to normalize data read from a file.

I have a data file called "test.dat" containing:
-------------
1 2
3 4
-------------

When I execute the code:
------------------------------
library("affy")

x <- read.table("test.dat", header=FALSE)
y <- as.matrix(x)
z <- matrix(c(1, 3, 2, 4), 2, 2)

print(normalize.quantiles(y))
print(normalize.quantiles(z))
----------------------

I get very strange results from the first print statement.

 > source("test.R")
                [,1]           [,2]
[1,] -1.067217e-314 -1.067217e-314
[2,]  1.384441e-291  1.384441e-291
      [,1] [,2]
[1,]  1.5  1.5
[2,]  3.5  3.5
 >

The values for the first normalization changes when I rerun it, so I 
suspect it might be caused by an invalid pointer dereference.  The 
normalize.quantiles is implemented in C in qnorm.c/R_qnorm_c.  
Unfortunately, I don't know how R passes around matrices around, so I 
cannot easily trace the problem further.  Has anyone seen this before?

I have attached the files "test.R" and "test.dat" containing the data 
above.  Please let me know if mailman has stripped it, and you would 
like me to send you a copy.

Thanks,
Jeff

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