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 -- =========================================== anjan purkayastha, phd bioinformatics analyst whitehead institute for biomedical research nine cambridge center cambridge, ma 02142 purkayas [at] wi [dot] mit [dot] edu 703.740.6939

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/tilingArra y/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