getdata                package:made4                R Documentation

_C_h_e_c_k _d_a_t_a_s_e_t

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

     This function is called by array2ade4 which converts input data
     into a  data.frame suitable for analysis in ADE4. This function is
     not normally  called by the user

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

     getdata(arraydata)

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

arraydata: a 'matrix', 'data.frame',  'exprSet' or 'marrayRaw'.   If
          the input is gene expression data in a 'matrix' or
          'data.frame'. The  rows and columns are expected to contain
          the variables (genes) and cases (array samples) 
          respectively.

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

     'bga' and other functions in made4 call this function and it is
     generally not necessary to call this directly.

     'array2ade4' calls 'getdata', and  will accept a
     'matrix','data.frame', 'exprSet'  or 'marrayRaw' format. It will
     also transpose data or add a integer to generate a positive data
     matrix. If the input data contains NA, these must first be removed
      or imputed (see the R libraries impute() or pamr()).  'getdata'
     is very similar  to 'getIntensityMatrix' in 'vsn'.

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

     Returns a data.frame suitable for analysis by ade4 or made4
     functions.

_N_o_t_e:

     This is not normally called by a user. Internal function.

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

     Aedin Culhane

_S_e_e _A_l_s_o:

     'array2ade4', 'getIntensityMatrix'

_E_x_a_m_p_l_e_s:

