Question: problem with siggenes

0

Edoardo Saccenti •

**130**wrote: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@cerm.unifi.it
www.cerm.unifi.it

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modified 14.7 years ago
by
Holger Schwender •

**900**• written 14.7 years ago by Edoardo Saccenti •**130**