normalise            package:BeadExplorer            R Documentation

_N_o_r_m_a_l_i_s_e _a _b_e_a_d_D_a_t_a _o_b_j_e_c_t

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

     Normalises a beadData object

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

     normalise(beadData, bkd = "Offset", offset = NULL, method = "Quantile", verbose = TRUE, ...)

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

beadData: An object of class 'beadData-class' 

     bkd: The background adjustment method to use - "Offset" or "Floor" 

  offset: A number represent the offset constant to use for background
          adjustment

  method: The normalisation method to be used - "Quantile", "Qspline",
          "RobustQuantile" or "None" 

 verbose: Logical, specifying whether commentray shouls be outputted 

     ...: Arguments passed to the normalisation function 

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

     Function to normalise a 'beadData-class' object.  Negative values
     are removed by the background adjustment option.   "Offset"  adds
     a constant to every intensity value - the default is to use the
     absolute smallest value on the array  so that no negative numbers
     remain.  The effect of adding a constant is to reduce the
     variability at low expression levels.  "Floor" sets all expression
     values less than 0.1 to 0.1.  This removes negative values but
     does not reduce the variability  at low expression levels.  The
     normalisation options are from the affy package.  See the affy
     help pages for more information.  To use normalised values from
     the BeadStudio output, select "None" for the normalisation.

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

     A normalised 'beadData-class' object

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

     Gareth Elvidge gareth.elvidge@well.ox.ac.uk

_R_e_f_e_r_e_n_c_e_s:

     affy help pages

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

     See Also as 'help'

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

     data(examplebeadData)
     normdata<-normalise(examplebeadData, bkd="Offset", offset=70, method="Qspline")

