if you have different numbers of peaks, bins, whatever, you will need to do
kernel smoothing to get the appropriate distribution of quantiles, then
normalize to that.  Pan Du implemented this in the 'lumi' package, FWIW.
 Personally I think it's a clever enough idea (kernel-smoothed quantile
normalization) that you should read it anyways, but...

If you just want to normalize equal numbers of bins, it is pretty
straightforward, e.g. suppose you have 100 runs of 100 bins/peaks/whatever
(key point being they all have the same number of things per run to
normalize ranks of):

library(preprocessCore)

par(mfrow=c(1,2))
foo <- matrix(rpois(10000, rgamma(1.5, 90)), ncol=100)
plot(density(foo[,1]), xlab='reads', main='before')
for(i in 2:100) lines(density(foo[,i]))

bar <- normalize.quantiles(foo)
plot(density(bar[,1]), xlab='reads', main='after')
for(i in 2:100) lines(density(bar[,i]))


sessionInfo()
## R version 3.0.0 (2013-04-03)
## Platform: x86_64-unknown-linux-gnu (64-bit)
##
## attached base packages:
## [1] stats     graphics  grDevices datasets  utils     methods   base
##
## other attached packages:
## [1] preprocessCore_1.23.0 BiocInstaller_1.11.1  gtools_2.7.1
## [4] devtools_1.2
##
## loaded via a namespace (and not attached):
## [1] digest_0.6.3   evaluate_0.4.3 httr_0.2       memoise_0.1
 parallel_3.0.0
## [6] RCurl_1.95-4.1 stringr_0.6.2  tools_3.0.0    whisker_0.3-2



On Tue, Jun 4, 2013 at 6:21 AM, Yashwant Kumar [guest] <
guest@bioconductor.org> wrote:

>
> I have to run preprocess core for qantile normalization of my data. Data
> has protein name in column and peak intensity in row.
>
> I have data of different time point. each time point has three replicates.
> I did all protein normalization for now but two time points are not
> behaving as expected. So I would like to do quantile normalization using
> for the data and this I don't want between replicates but between time
> points.
>
> Please advise me how to do this. I can run R if you will explain me to
> matrix preparation.
>
> Best regards,
> Yashwant
>
>  -- output of sessionInfo():
>
> no
>
> --
> Sent via the guest posting facility at bioconductor.org.
>
> _______________________________________________
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>



-- 
*A model is a lie that helps you see the truth.*
*
*
Howard Skipper<http://cancerres.aacrjournals.org/content/31/9/1173.full.pdf>

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