[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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