normalizeByReference       package:tilingArray       R Documentation

_P_r_o_b_e-_s_p_e_c_i_f_i_c _n_o_r_m_a_l_i_z_a_t_i_o_n _o_f _h_y_b_r_i_d_i_z_a_t_i_o_n _i_n_t_e_n_s_i_t_i_e_s _f_r_o_m _a _s_h_o_r_t-_o_l_i_g_o _m_i_c_r_o_a_r_r_a_y

_D_e_s_c_r_i_p_t_i_o_n:

     Adjust the hybridization intensities from a short oligo microarray
     for probe-specific response effect by using one or several
     reference hybridizations.

_U_s_a_g_e:

     normalizeByReference(x, reference, pm, background, nrStrata=10,
       cutoffQuantile=0.05, plotFileNames, verbose=FALSE)

_A_r_g_u_m_e_n_t_s:

       x: eSet containing the data to be normalized.

reference: eSet with the same number of features as 'x', containing the
          reference signal.

      pm: indices specifying the perfect match features in 'reference'.
          This can be either an integer vector with values between 1
          and 'nrow(exprs(reference))' or a logical vector.

background: indices specifying a set of background features in 'x'.
          This can be either an integer vector with values between 1
          and 'nrow(exprs(x))' or a logical vector.

nrStrata: Integer (length 1), number of strata for the estimation of
          the background function.

cutoffQuantile: Numeric (length 1), the probes whose reference signal
          is below this quantile are thrown out.

plotFileNames: Character vector whose length is the same as the number
          of arrays in 'x'. Optional, if missing, no plots are
          produced.

 verbose: Logical of length 1, if 'TRUE', some messages about progress
          are printed.

_D_e_t_a_i_l_s:

     The intensities in 'x' are adjusted according to the reference
     values. For example, the reference values could be obtained by
     hybridizing a DNA sample to the array. The abundance of target is
     thus the same for all PM probes, and the intensities that are
     actually observed can be used for estimating the adjustment
     parameters. Since this only makes sense for the PM probes, NA
     values be returned for all other probes. The set of indices for
     background probes, 'background', is used for the estimation of the
     background correction.

_V_a_l_u_e:

     A copy of 'x' with the normalized intensities.

_A_u_t_h_o_r(_s):

     W. Huber huber@ebi.ac.uk

_R_e_f_e_r_e_n_c_e_s:

     Transcript mapping with  oligonucleotide high-density tiling
     arrays, W. Huber, J. Toedling, L. Steinmetz, preprint (2006).

_E_x_a_m_p_l_e_s:

       ## see vignette assessNorm.Rnw in inst/scripts directory

