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',  'ExpressionSet' 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',
     'ExpressionSet' 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'

