[BioC] Post rma analysis

Adaikalavan Ramasamy gisar at nus.edu.sg
Wed Aug 20 12:14:01 MEST 2003

Dear all,

I have performed rma() on several CEL files. Here is the summary of this
expression data :

    Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
   2.674   5.021   6.150   6.144   7.151  14.420 

The mean and variance of all arrays/columns are very close. A boxplot
shows that the arrays are on comparable scales.

However, these values are all positive. Do we take the log2
transformation followed by column median centering or use these rma
output ? I am worried that this might make a difference if we use t-test
or any other parametric tests.

Can anyone help me ? Many thanks.

Regards, Adai

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