[BioC] [Fwd: fold change calculation]

[Richard Pearson]

Paul

You don't say which package you're using, but I guess this is 
simpleaffy? If so, looking at the help page 
(?get.fold.change.and.t.test) would have told you:

"The fold-changes are computed from the average values across 
replicates. By default this is done using the mean of the unlogged 
values. The parameter, method allows the mean of the logged values or 
the median to be used instead. T-tests are always computed with the 
logged data."

Of course, if you don't want to believe the documentation, you can 
always look at the source code :-)

Fold change is simply A-B (if on the log scale), or A/B (if on raw scale).

Regards

Richard.


Paul Hammer wrote:
>
>
> ------------------------------------------------------------------------
>
> Subject:
> fold change calculation
> From:
> Paul Hammer <Paul.Hammer at p-t-p.de>
> Date:
> Tue, 19 Feb 2008 19:02:52 +0100
> To:
> Sean Davis <sdavis2 at mail.nih.gov>
>
> To:
> Sean Davis <sdavis2 at mail.nih.gov>
>
>
> dear members,
>
> could anyone explain or give me the exactly formula of the fold change 
> calculation?
>
> R code
> -------------------------------------
> >  get.fold.change.and.t.test(rma.affy[PDE1A_exon_probesets], 
> "tissue", c("prostate", "breast"), method="logged")
>
> > An object of class PairComp
>
>        prostate   breast
> 2590606 6.237610 4.900560
> 2590612 7.878071 6.961996
> 2590628 4.065403 3.468860
> 2590599 3.854438 3.560036
> 2590615 4.806831 4.309884
> 2590586 1.102444 1.214922
> 2590618 3.314213 3.310029
> 2590608 4.184283 2.767696
> 2590611 5.382736 4.669508
> 2590601 2.871831 2.427491
> 2590617 7.057866 6.922251
> 2590591 3.842315 2.792450
> 2590607 4.448152 3.377348
> 2590613 7.148809 6.013015
> 2590645 4.882622 5.073177
> 2590600 2.777127 3.181344
> 2590616 4.407165 4.127747
> 2590619 1.623058 1.946055
>
> Slot "fc":
>     2590606      2590612      2590628      2590599      2590615      
> 2590586
> 1.337049955  0.916074705  0.596543177  0.294402317  0.496947309 
> -0.112478340
>     2590618      2590608      2590611      2590601      2590617      
> 2590591
> 0.004183895  1.416586498  0.713228192  0.444339972  0.135614697  
> 1.049865355
>     2590607      2590613      2590645      2590600      2590616      
> 2590619
> 1.070804709  1.135794462 -0.190555504 -0.404217037  0.279418232 
> -0.322996530
>
> ....
>
> thanks
> paul
>
>
> ------------------------------------------------------------------------
>
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