[BioC] data transformation

[Rohit Ghai]

hello all
I am trying to perform VSN normalization with one-color Codelink chip data.
after normalization in vsn i start getting negative values all over the 
expression
matrix... this makes it difficult to get fold changes for the genes. how 
can i get
around this problem ? I think its because the raw intensity values i get 
from codelink
are a bit low. I also multiplied the raw data matrix by a factor of 2. 
With the trasnformed
data matrix VSN did not give any negative values, but the boxplots 
looked a little upward shifted
as compared to the non-trasnformed data. The final gene list that I got 
(genes with a standard
deviation of more than 2 in any experiment) was the same both with the 
raw data and with the
transformed data.. but I want to know if its alright to do this?
any ideas would be appreciated

Rohit