[BioC] fraction or difference

[Mark Cowley]

Hi Yolande,
Are your protein counts on the log, or linear scale? If log, use difference, if linear, use fraction,
HTH
Mark

On 13/11/2010, at 3:07 AM, Yolande Tra wrote:

> Hi list members,
> 
> May I have your expert opinion on the following.
> I am looking for protein differentially expressed due to treatment of
> a certain disease. Protein counts were measured before and after
> treatment was given. Some patients respond to the treatment
> (responders) and got better and some patients did not respond to the
> treatment (nonresponders). The goal is to find which protein is
> responsible for the positive response, so really looking at group
> factor.
> I have used two quantities to describe the change of these proteins:
> ratio (after/before) and difference (after-before). After computing
> these quantities, I considered the design as two independent groups
> (responders versus nonresponders).
> I used rankproduct procedure to detect the proteins of interest. I
> obtained different lists of protein differentially expressed which
> means that using different quantities afftect the results.
> 
> My question is which quantity (fraction or difference) is more
> sensitive to a change in this situation?
> 
> Thank you for any suggestion and any insight in this question,
> Yolande
> 
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