ITALICS (version 2.32.0)

trainITALICS: ITALICS training

Description

Estimation of the quartet effect based on several normal sample chips

Usage

trainITALICS (dir,  amplicon=2.1, deletion=-3.5, deltaN=0.15, forceGL=c(-0.2,0.2), param=c(d=2), nbsigma=1, ...)

Arguments

dir

The directory containing the normal sample chips. All theses chips should be of the same type hind, xba, nsp or sty. Only .CEL files be considered

amplicon

see the amplicon parameter in the daglad function

deletion

see the deletion parameter in the daglad function

deltaN

see the deltaN parameter in the daglad function

forceGL

see the forceGL parameter in the daglad function

param

see the param parameter in the daglad function

nbsigma

see the nbsigma parameter in the daglad function

...

Other daglad parameters.

Value

• a data.frame with two column fsetid and quartetEffect

source

Institut Curie, [e-mail].

Details

The ITALICS function take into account a quartet effect which is computed on a reference data set of normal women samples. The ITALICSData provide quartetEffect for the Xba, Hind, Sty and Nsp chip computed on our own reference data set.

We recommand that you use your own reference data set to compute the quartet Effect by using the trainITALICS function. ITALICS reference data should contain only woman normal samples. Furthermore we recommand that you check that none of these chip have obvious spatial artifact. To so read the cel files using the read.affybatch (form the affy package). Then use the image function on the obtain affybatch object.