[BioC] multtest on human intervention study

[Hinnerk Boriss]

Hi Kevin,
did you do in vitro amplification of your samples to increase the cRNA
available for hybridization? This is a common source of the problem you
are describing. There are no mathematical methods for retrofixing this
problem.

> Q1: Do you have any arguments against the RMA(after)-RMA(before)
approach?
With RMA you loose some of your differentially expressed genes. If your
intensities on the chip are not all on the very low end, VSN does a much
better job.

> RMA is a logarithm, so the difference should express a fold change.
Almost, its the log ratio. Fold change is the log-ratio +1 or -1,
respectively.
> 
> Q2: Do you have another method for similar situations when the
> patient-to-patient variance is bigger than the treatment effect?
Can you do the measurements on the same patients: like before and after?
In that case you should used paired t-tests. They account for that
problem. 
> 
> Q3: Seven tests say NO, is it really a NO? Should I conclude that the
> treatment was ineffective?
First, you have to sort out your technological problems. If all stays
the same afterwards, you have an indication for ineffectiveness. Not
more.

> Q4: Can you suggest another method that is more likely to 
> find a "real" change in response to treatment.
Could you plot the standard error of your estimator for the difference
versus the absolute value of this estimator? This could help in deciding
if there is more in store for you.


Cheers,
Hinnerk