[BioC] Error message from running SAM for one-class case(siggenes)

[Fangxin Hong]

Hi there:
I tried to run SAM for one-class case , using package siggenes.
(R 1.9.1, siggenes Version: 1.0.6)

My data set contains 2000 genes with 4 replications. I got the following
error message:
--------------------------
Warning: There are 2000 genes which have variance Zero or no non-missing
values.
         The d-value of these genes is set to NA.

Error in var(v) : missing observations in cov/cor
--------------------------------
I checked siggenes vignette, they didn't out down any example for
one-class study. I tried to use the data(golub)(used as example in the
vignette)  to do one-sample case as following
-------------------------------------
> temp=sam(golub[,1:10],golub.cl[1:10],rand=123)
SAM Analysis for the one-class case.

Warning: Expected classlabel is 1. cl will thus be set to 1.

Warning: There are 1041 genes which have variance Zero or no non-missing
values.
         The d-value of these genes is set to NA.

Error in var(v) : missing observations in cov/cor
----------------------------
Although this is not an appropriate data set for one-class study, but SAM
should still work. Anybody has idea about this, I would appreciate for any
hint.
BTW, I used Excel SAM program before, it was OK for this kind one-class
study.

Thank you all!
Fangxin




-- 
Fangxin Hong, Ph.D.
Plant Biology Laboratory
The Salk Institute
10010 N. Torrey Pines Rd.
La Jolla, CA 92037
E-mail: fhong at salk.edu