[BioC] normalization the expression values

[Assa Yeroslaviz]

hello,

I'm not sure if this is the right platform to try and look for information about
my problem, but I've serached the internet (google) and didn't find anything
helpful.

While trying to find significant genes in my data I used two sets of matrices.
the frist one is directly from the affymetrix chips and the second one is a
matrix of the natural logarithm from the same chips.

What i need is bit of backgroung infromation. Does it make sense to logarithmise
the  expression values?

I've tried both variants and got almost the same results, but not exactly the
same. Does it has anything to do with the distribution of the two matrices,
which differ greatly from each other?

which matrix should one use? (can i ask such a question?)

I'll be happy to get any help at all. If anyone knows a good book or an article
where I can get some information about these themes, I'll be happy to know.

THX,

Assa
-- 
Assa Yeroslaviz
Lötzenerstr. 15
51373 Leverkusen