[BioC] Normalisation of focussed arrays and Taq-man gene cards
Aedin
aedin.culhane at ucd.ie
Mon Sep 13 19:51:01 CEST 2004
Dear BioC
What is currently considered the best method of normalisation where the
assumption that most genes are unchanged is invalid? Is it best to apply
the Li & Wong algorithm or are there other methods that I should consider?
I wish to normalise and analyse the following:
1. A focussed oligonucleotide array. Although this included a good number
invariant "control" genes, most of the genes on the arrays are expected to
change.
2. Arrays in which methylating agents are studied, again a large number
genes on the array are expected to change.
3. Taqman RT-PCR cards.
I would be grateful if you could tell me if I need to consider different
methods for:
A. oligonucleotide single channel focused arrays,
B. dual channel spotted focussed arrays
Thanks a million for your advice in this. I appreciate your help.
Best wishes
Aedin
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