[BioC] Determining Synergy in MA expts

[Adaikalavan Ramasamy]

What you are looking for is called "interaction" in statistics and the
design of your experiment is described as a 2x2 factorial design. This
is also sometimes described as two-way ANOVA (analysis of variance).

You will need to ensure that the data follows a normal distribution
(e.g. by taking log2) in order to use this method as it assumes normally
distributed error terms.

Trying reading up 
 http://www.uwsp.edu/psych/stat/13/anova-2w.htm
 http://www.bioconductor.org/repository/devel/vignette/factDesign.pdf


PS : Another reason why statisticians like logged values is that it is
symmetric around 1. E.g. raw values of 0.5 and 2.0 are -0.693 and 0.693
on log scales.

Regards, Adai



On Tue, 2005-11-08 at 11:55 -0500, Lance Palmer wrote:
> I am interested to know how one may determine if two conditions can have
> synergistic effects.  For example, lets say we expose cells to two
> conditions, X and Y.  We have four microarray chips.  
> 
>  
> 
>             0          X          Y          X+Y
> 
>  
> 
> Lets suppose the following raw data
> 
>  
> 
>             8          2046     16        4096
> 
>  
> 
> Log2 of those numbers
> 
>  
> 
>             3          11        4          12
> 
>  
> 
> Log fold change vs no stimuli
> 
>  
> 
>                         8          1          9
> 
>  
> 
> Fold change
> 
>  
> 
>                         256       2          512
> 
>  
> 
> Raw change
> 
>  
> 
>                         2038     8          4088
> 
>  
> 
> 
> 
> 
> 
> If you look at the fold change one can say there is no synergistic effect
> since the log fold change of 9 can be explained by the 2**8 increase and the
> 2**1 increase.  (or I could say the 512 comes from the 256x component and 2x
> component)
> 
>  
> 
> If you look at the raw change, it appears to be synergistic since
> 2038+8<<<4088.
> 
>  
> 
> I am not a mathematician so I don't know which would be the proper way to
> look at this.  Would an example like this be synergistic.  And what is the
> best way to approach this.
> 
>  
> 
> 
> 
> 
> 	[[alternative HTML version deleted]]
> 
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
>