trainITALICS             package:ITALICS             R Documentation

_I_T_A_L_I_C_S _t_r_a_i_n_i_n_g

_D_e_s_c_r_i_p_t_i_o_n:

     Estimation of the quartet effect based on several normal sample
     chips

_U_s_a_g_e:

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

_A_r_g_u_m_e_n_t_s:

     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.

_D_e_t_a_i_l_s:

     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.

_V_a_l_u_e:

a data.frame with two column fsetid and quartetEffect: 

_N_o_t_e:

     People interested in tools dealing with array CGH analysis and DNA
     copy number analysis can visit our web-page <URL:
     http://bioinfo.curie.fr>.

_A_u_t_h_o_r(_s):

     Guillem Rigaill, italics@curie.fr.

_S_o_u_r_c_e:

     Institut Curie, italics@curie.fr.

