[R] Question regarding analysis of normalised data

From: Ulrik Stervbo <ulriks_at_ruc.dk>
Date: Wed 11 Oct 2006 - 07:05:34 GMT

Dear all,

I want to see if the treatment of an animal with a specific compound has an effect on the expression of certain genes. Though my question is based in biology, it really is all about how to deal with the standard deviation in normalised data.

I have three groups of animals; untreated, treated with placebo, and treated with a single concentration of the compound in question.

Gene expression is measured in triplicate, that is I have three values for each measurement of each animal, and normalised to a standard gene.

My problem is, that there is no guarantee that one of the measurements of either the gene in interest or the standard gene does not fail, so I need to take the relative means of the triplicates, but what to do with the standard deviations?

Also, I need to calculate fold difference in the normalised means between the groups of animals - again; how do I handle the standard deviation?

And finally, how do I calculate significant differences between the groups?

Thanks in advance for any help and suggestions Ulrik

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