[BioC] problem with siggenes

[michael watson (IAH-C)]

As far as I know, if you only have two arrays, one from each "treatment" in your experiment, there is no way that you can do any kind of statistics at all....

-----Original Message-----
From: bioconductor-bounces at stat.math.ethz.ch [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Edoardo Saccenti
Sent: 13 January 2005 16:45
To: bioconductor at stat.math.ethz.ch
Subject: [BioC] problem with siggenes


I would like to manage a FDR analysis via
SAM as implemented in siggenes package.

First I read 2 file.CEL into an affybatch object called "mydata" Then i used rma routine to correct my data obtaining an exprSet object called "myeset"

According to the guide I need to pass to sam
the data (myeset in this case) and a vector cl

This is a one class case,  so 
so cl must be a vector of ones of length equal to number
of sample.
As the number of sample is 2 (2 CEL files)

cl <- c(1,1)

Typing at the R prompt:

	out <- sam.dstat(myeset, cl, rand=123)

I get the following:

	We're doing 4 complete permutations
	Error in rowSums(x, prod(dn), p, na.rm) : invalid value of n
	In addition: Warning message:
	There are 147 genes with zero variance. These genes are removed,
	and their d-values are set to NA.

I'm sure I'm doing some stupid mistake 'couse I'm new to R and BioC: nevertheless can anybody help me?

Thanks
edoardo



"Raffiniert ist der Herr Gott,
 aber boshaft ist Er nicht."

---
Dr. Edoardo Saccenti
FiorGen Pharmacogenomics Foundation
CERM Nuclear Magnetic Resonace Research Center
Scientific Pole - University of Florence
Via Luigi Sacconi n° 6
50019 Sesto Fiorentino (FI)
tel: +39 055 4574193
fax: +39 055 4574253
saccenti at cerm.unifi.it
www.cerm.unifi.it

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