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.

