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

