[BioC] fraction or difference

[Yolande Tra]

Thanks. Yolande.

On Sun, Nov 14, 2010 at 5:34 PM, Mark Cowley <m.cowley at garvan.org.au> wrote:
> 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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>
>