[BioC] SAM in siggenes package

[James MacDonald]

In my version of siggenes, I don't see any variables called x and y that
can be passed to the function sam. If RG.all contains all the data you
wish to compare, you only need to pass this data.frame along with a
vector of classlabels that identify which class each column of data
belongs to. If you are doing a two-class unpaired analysis, this will be
a vector of 0s and 1s. If paired, then paired integers from 1:n, and if
oneclass, a vector of 1s.

HTH,

Jim



James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623

>>> "Anna Cao" <yunie at caltech.edu> 12/19/03 01:50PM >>>
Hi,

I'm trying to run SAM using the siggenes package in R (version 1.8.1
in
Window XP). I have a 16247x204 matrix containing all the arrays in my
experiment. This matrix includes several experimental conditions
including
replicates. I need to run sam for each experimental condition. I try
the
following command and got this error. 

sam(RG.alls, x=RG.alls$R[1:16], y=RG.alls$G[1:16])
Error in as.double.default(structure(list(structure(c(NA, NA, NA, NA, 
: 
        (list) object cannot be coerced to double

I assume this error may be related to all the blank (NA) points I have
in
the matrix. Are there any ways to remove these empty spots for each set
of
replicates without having to export and arrange the matrix elsewhere?

Anna

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