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_n _o_l_i_g_o_n_u_c_l_e_o_t_i_d_e _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 an oligonucleotide
     microarray for probe-specific response effect by using one or
     several reference hybridizations. If 'x' contains more than one
     array, 'vsnMatrix' from the 'vsn' package is called for between
     array normalization.

_U_s_a_g_e:

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

_A_r_g_u_m_e_n_t_s:

       x: ExpressionSet containing the data to be normalized.

reference: ExpressionSet with the same number of features as 'x',
          containing the reference signal, on the raw scale
          (non-logarithmic). This argument can be used to directly
          input the data from a set of replicate DNA hybridizations.
          Alternatively, the argument 'refSig' can be specified.

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

  refSig: A numeric vector of the same length as 'pm' with estimates of
          probe response effects, on a logarithm-like scale. This
          argument can be specified alternatively to 'reference'.

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. Typically, the reference values are obtained by
     hybridizing a DNA sample to the array, so that the abundance of
     target is the same for all reference probes, and their signal can
     be used to estimate the probe sequence effect. A reference probe
     is a probe that perfectly matches the target genome exactly once.
     Usually, not all probes on a chip are reference probes, hence the
     subset of those that are is specified by the argument 'pm'.

     The background signal is estimated from the probes indicated by
     the argument 'background'. They need to be a strict subset of the
     'reference' probes. I.e., they need to uniquely match the target
     organism's DNA, but are not expected to match any of its
     transcripts. A robust estimation method is used, so a small
     fraction of 'background' probes that do hit transcripts is not
     harmful.

     A limitation of this normalization method is that it only makes
     sense for the data from reference probes, NA values are returned
     for all other probes.

     The functions 'PMindex' and 'BGindex' can be used to produce the
     'pm' and 'background' arguments from a 'probeAnno' environment
     such as provided in the davidTiling package.

     To summarize, a reference probe (indicated by argument 'pm') is a
     probe that perfectly matches the target genome exactly once, a
     background probe (indicated by argument 'background') is a
     reference probe which we expect not to be transcribed. These
     should not be confused with what is called 'perfect match' and
     'mismatch' probes in Affymetrix annotation.

_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:

     Huber W, Toedling J, Steinmetz, L. Transcript mapping with
     high-density  oligonucleotide tiling arrays. Bioinformatics 22,
     1963-1970 (2006).

_S_e_e _A_l_s_o:

     'PMindex', 'BGindex'

_E_x_a_m_p_l_e_s:

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

