avedups                package:limma                R Documentation

_A_v_e_r_a_g_e _O_v_e_r _D_u_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:
     avedups(x, ndups=2, spacing=1, weights=NULL)
     ## S3 method for class 'MAList':
     avedups(x, ndups=x$printer$ndups, spacing=x$printer$spacing, weights=x$weights)

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

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

   ndups: number of within-array replicates for each probe.

 spacing: number of spots to step from a probe to its duplicate.

 weights: numeric matrix of spot weights.

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

     A new data object is computed in which each probe is represented
     by the (weighted) average of its duplicate spots. For a 'MAList'
     object, the components 'M' and 'A' are both averaged in this way.

     If 'x' is of mode '"character"', then the duplicate 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 '1/ndups' as many
     rows.

_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.

