[BioC] tilingArray question

[Wolfgang Huber]

Anjan Purkayastha ha scritto:
>  From Huber et al, Bioinformatics 22 (16) 2006, 1963-1970, it appears 
> that parameters ci, di and delta need to be estimated from the data by 
> the user using the vsn package.  Is this assumption correct? Or does the 
> tilingArray package estimate these parameters from the data without any 
> user intervention?
> Tia,
> Anjan
> 


Dear Anjan,

these parameters are estimated for you by the normalizeByReference 
function, you don't need to do anything else.

Try having a look at:
https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/tilingArray/R/normalizeByReference.R
(user: readonly  password: readonly) and in particular the block in the 
end that is headed:
    ## call vsn, if there are >= 2 arrays

Hope this helps.
  Best wishes
	Wolfgang

----------------------------------------------------
Wolfgang Huber, EMBL-EBI, http://www.ebi.ac.uk/huber