[BioC] normalize.quantiles function not recognized by R

[Steve Lianoglou]

Hi Radhika,

On Jun 30, 2009, at 5:34 PM, Radhika Ambatipudi wrote:

> Hi
>
> I am very new to R. I am trying to normalize 4 sample sets of CEL data
> generated by using Tiling array. I think I have loaded all required  
> packages
> but when I call normalize.quantiles function in R, I get an error  
> message :
> Error: could not find function "normalize.quantiles". Can somebody  
> please
> help.


The "normalize.quantiles" function is in the preprocessCore library,  
which needs to be loaded first, like so:

=====
R> library(preprocessCore)
R> ...
R> ny.data.qq <- normalize.quantioes(my.data)
=====

Since you're new to R, one way you could have discovered this is by  
using the "help.search" function, eg:

=====
R> help.search('normalize.quantiles')

Help files with alias or concept or title matching
‘normalize.quantiles’ using regular expression matching:


preprocessCore::normalize.quantiles
                         Quantile Normalization
preprocessCore::normalize.quantiles.in.blocks
                         Quantile Normalization carried out separately
                         within blocks of rows
preprocessCore::normalize.quantiles.robust
                         Robust Quantile Normalization
preprocessCore::normalize.quantiles.use.target
                         Quantile Normalization using a specified target
                         distribution vector


Type '?PKG::FOO' to inspect entry 'PKG::FOO TITLE'.
=====

Hope that helps,
-steve

--
Steve Lianoglou
Graduate Student: Physiology, Biophysics and Systems Biology
Weill Medical College of Cornell University

Contact Info: http://cbio.mskcc.org/~lianos/contact