array2ade4               package:made4               R Documentation

_C_o_n_v_e_r_t_s _m_i_c_r_o_a_r_r_a_y _i_n_p_u_t _d_a_t_a _i_n_t_o _a _d_a_t_a _f_r_a_m_e _s_u_i_t_a_b_l_e _f_o_r _a_n_a_l_y_s_i_s
_i_n _A_D_E_4.

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

     Converts input data into a data.frame suitable for analysis in
     ADE4. This function is called by 'bga' and other made4 function.

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

     array2ade4(dataset, pos = FALSE, trans = FALSE)

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

 dataset: 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. 

     pos: Logical indicating whether to add an integer to 'dataset', to
          generate positive 'data.frame'. Required  for 'dudi.coa' or
          'dudi.nsc'.

   trans: Logical indicating whether 'dataset' should be transposed.
          Default is 'FALSE'.

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

     'bga' and other functions in made4 call this function and it is
     generally *not* necessary to call 'array2ade4' 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 missing values (NA), these must first
     be removed or imputed (see the R libraries impute() or pamr()).

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

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

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

     Aedin Culhane

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

     'getdata', 'getIntensityMatrix'

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

     library(affy)
     data(geneData)
     class(geneData)
     dim(geneData)
     dim(array2ade4(geneData))
     class(array2ade4(geneData))

