Dear all,

For whom is familiar with Agilent gene expression data, I would like to
ask help.

We recently received some Agilent gene expression data from our
collaborators. For individual sample, there are 7 corresponding columns:

  Unknown:Log(Ratio)  Unknown:Ratio  Unknown:Fold Change  Unknown:Log(Error)
Unknown:P-Value  Unknown:Intensity 1  Unknown:Intensity 2
It seems that Ratio= Intensity1/Intensity2. I wonder whether I should use
log2(Ratio) or Log(Ratio) or just Ratio for further analysis. Besides, why
should Ratio be calculated as Intensity1/Intensity2 instead of
Intensity2/Intensity1?

Thank you very much for your help in advance!

Sincerely,
      Allen

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