medianNormalise          package:beadarray          R Documentation

_M_e_d_i_a_n _n_o_r_m_a_l_i_s_e _d_a_t_a _i_n _a _m_a_t_r_i_x

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

     Normalises expression intensities so that the intensities or
     log-ratios have equal median values across a series of arrays
     (columns).

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

     medianNormalise(exprs, log=TRUE)

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

   exprs: a matrix of expression values

     log: if TRUE then do a log2 transformation prior to normalising

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

     Normalisation is intended to remove from the expression measures
     any systematic trends which arise from the microarray technology
     rather than from differences between the probes or between the
     target RNA samples hybridized to the arrays.

     For median normalisation, the intensity for each gene is adjusted
     by subtracting the median of all genes on the array and then
     adding the median across all arrays. The effect is that each array
     then has the same median value.

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

     Produces a matrix of normalised intensity values (on the log2
     scale by default) with the same dimensions as 'exprs'.

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

     Mark Dunning

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

     data(BSData)
     BSData.med = assayDataElementReplace(BSData, "exprs", medianNormalise(exprs(BSData)))

