[BioC] Variance of M as a function of A in MA plots

Rafael A. Irizarry ririzarr at jhsph.edu
Thu May 22 18:24:31 MEST 2003


ive oberved exactly the oposite. SDs for RMA,dCHip and MAS 5.0 depend on 
A. but MAS 5.0 is by way more dependent. look at 

http://www.biostat.jhsph.edu/~ririzarr/sd.html

for some pictures.

keep in mind that RMA gives back log2 values. expresso with mas gives back 
linear scale values. 


On Thu, 22 May 2003, Andrew Harrison wrote:

> Hi,
> 
> 	I've generated several MA/RI plots after using RMA and 
> noticed that the standard deviation in M (fold change) is related 
> to A (average intensity) - to derive the SD in M, only sample fold 
> changes over a limited range in A (a similar calculation to the 
> Quackenbush sliding Z-score). 
> 
> 	When using RMA, the standard deviation in M is proportional 
> to A, except for the largest intensities. However, when using 
> expresso with all the options set to MAS, the standard deviation is 
> independent of A. I believe the variance in M should be independent 
> of A, in which case this suggests MAS is the way to go.
> 
> 	Has anybody else seen this effect, or can suggest a remedy,  
> or more likely a gap in my logic?
> 
> 	Best wishes and thanks in advance,
> 		Harry
> 
>



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