[BioC] other timimg questions

[Rob Dunne]

Hi list,
       with the discussion of (gc)rma times, I
thought it might be opportune to aske what other people
are doing about the  speed of loess in bioconductor 1.2.

for 54 arrays I get a time of over 4 hours (I stopped the process
then). After experimenting with the parameters in the code I have 
gone back to an older version. So far this has caused no problems.

Gordon Smyth has suggested going to limma. What are other 
people doing?



>marrayNorm 1.1.3   (installed with bioconductor 1.2)
> > unix.time(experiment1.norm<-maNorm(experiment1, norm="loess"))
>Timing stopped at: 15358.18    19.85 20734.47     0.00     0.00
>
>ie I interrupted the process -
>but with  marrayNorm 1.1.1 reinstalled
>
>  marrayNorm 1.1.1
> > unix.time(experiment1.norm<-maNorm(experiment1, norm="loess"))
>[1] 803.99  29.73 843.40   0.00   0.00
>

-- 
Rob Dunne         Fax: +61 2 9325 3200     Tel: +61 2 9325 3263
CSIRO Mathematical and Information Sciences     +61 2 9325 3100
Locked Bag 17, North Ryde, New South Wales, Australia, 1670         
http://matilda.vu.edu.au/~dunne  Email: Rob.Dunne at csiro.au

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