Dear all,
I have some basic questions about two-color array.
For two-color array with common reference method, one color is for
interested sample and the other is for common reference. Generally, the
output is the ratio between interested sample and common reference sample
after a Lowess method.
1) Can I simply regard these ratios as gene expression values (used in
one-color array) and directly use them to do some analysis since a common
reference is used? Or I have to calculate the expression value of
interested sample from raw data (onlyl use one channel)?
2) Should I do some inter-chip normalization such as Quantile method used
in one-colar array?
3) Should I check the batch effect? Is there popular or standard method to
check and alleviate bache effect?
Thank you very much.

Feng

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