erankProdAltSpl        package:oneChannelGUI        R Documentation

_I_m_p_l_e_m_e_n_t_a_t_i_o_n _o_f _t_h_e _R_a_n_k _P_r_o_d_u_c_t _m_e_t_h_o_d _f_o_r _t_h_e _d_e_t_e_c_t_i_o_n _o_f _a_l_t_e_r_n_a_t_i_v_e _s_p_l_i_c_i_n_g _e_v_e_n_t_s

_D_e_s_c_r_i_p_t_i_o_n:

     This is a graphical interface to the RP function from RankProd
     package applied to detection of alternative splicing

_U_s_a_g_e:

     erankProdAltSpl()

_D_e_t_a_i_l_s:

     Before using this method it is strongly suggested to perform a
     filter on the basis of DABG p-values using  the filtering function
     available in the filtering menu. DABG values can be calculated if
     exon array probe set data are generated using the oneChannelGUI
     graphical implementation to APT tools. Affymetrix suggests to
     calculate probe set intensity at gene level using iterPlier and at
     exon level using plier. Subsequently SpliceIndex need to be
     calculated using the function available in the exon menu. Finally
     the Rank Product method could be applied exon by exon. For more
     details on the method see RankProd package. Selection of putative
     alternative splicing could be done using the filtering function
     available in the filtering menu of  oneChannelGUI

_N_o_t_e:

     IMPORTANT we are still evaluating the efficacy of this method for
     detection of alternative splicing events. Use it being concious of
     this!

_A_u_t_h_o_r(_s):

     Raffaele A Calogero

_S_e_e _A_l_s_o:

     inspecting.splice, spliceIndex

