[BioC] SAM and siggenes packages

[James MacDonald]

All this error means is that for 353 genes, the log ratio is the same
for all samples. If the log ratio is the same for all samples, the
variance is zero, so your t-statistic will have a zero in the
denominator. Since that will result in an infinite value for the
t-statistic, siggenes simply returns an NA.

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

>>> perin <perin at cirad.fr> 04/26/04 01:07PM >>>
Hi,

I'am new on this mailing list and I probably have a 'stupid' question.
I'am doing SAM analysis for the one-class case on a 6 replicates per 
8448 gene matrix.
I get each time this message

SAM Analysis for the one-class case.
 
Warning: There are 353 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

Any idea ?

Here the code:

sam.output<-sam(salt_stress,salt.cl)

where salt.cl<-c(rep(1,6))
and salt_stress a matrix (6 col per 8448 row)


thanks




Thanks

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