avereps                package:limma                R Documentation

_A_v_e_r_a_g_e _O_v_e_r _I_r_r_e_g_u_l_a_r _R_e_p_l_i_c_a_t_e _S_p_o_t_s

_D_e_s_c_r_i_p_t_i_o_n:

     Condense a microarray data object so that values for within-array
     replicate spots are replaced with their average.

_U_s_a_g_e:

     ## Default S3 method:
     avereps(x, ID=rownames(x))
     ## S3 method for class 'MAList':
     avereps(x, ID=NULL)

_A_r_g_u_m_e_n_t_s:

       x: a matrix-like object, usually a matrix or an 'MAList' object.

      ID: probe identifier.

_D_e_t_a_i_l_s:

     A new data object is computed in which each probe is represented
     by the average of its replicate spots. For an 'MAList' object, the
     components 'M' and 'A' are both averaged in this way, as 'weights'
     and any matrices found in 'object$other'.

     For an 'MAList' object, 'ID' defaults to 'MA$genes$ID' is that
     exists, otherwise to 'rownames(MA$M)'.

     If 'x' is of mode '"character"', then the replicate values are
     assumed to be equal and the first is taken as the average.

_V_a_l_u_e:

     A data object of the same class as 'x' with a row for each unique
     value of 'ID'.

_A_u_t_h_o_r(_s):

     Gordon Smyth

_S_e_e _A_l_s_o:

     'dimnames' in the base package.

     02.Classes gives an overview of data classes used in LIMMA.