normQpcrRankInvariant        package:qpcrNorm        R Documentation

_F_u_n_c_t_i_o_n _f_o_r _R_a_n_k-_I_n_v_a_r_i_a_n_t _S_e_t _N_o_r_m_a_l_i_z_a_t_i_o_n _f_o_r _q_P_C_R _D_a_t_a.

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

     Implements rank-invariant set normalization for a 'qpcrBatch'
     object.  We have adapted this algorithm from the function
     'normalize.invariantset'   from the 'affy' package.

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

     normQpcrRankInvariant(qBatch, refType, rem.highCt = FALSE, thresh.Ct = 30)

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

  qBatch: A 'qpcrBatch' object. 

 refType: Indicates what reference sample should be used, can be an
          integer or character string. See Details below. 

rem.highCt: Logical indicator, TRUE if user wishes to remove genes with
          high Ct values (very low expression)  that may be associated
          poor data quality. 

thresh.Ct: Numerical value indicating the Ct value cutoff threshold, if
          'rem.highCt' = FALSE,  genes with Ct values > thresh.Ct are
          removed from the data set.   

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

     The algorithm computes all rank-invariant sets of genes between
     pairwise comparisons where each  experimental sample in the
     'qpcrBatch' object is paired against a reference. There are
     several ways to specify  what a sensible choice for the reference
     sample should be. 

      1. The reference is an experimental sample in the 'qpcrBatch'
     object. 
      Specify 'refType' as an 'integer' value, corresponding to the
     index of which experimental sample is the reference.  

      2. The reference is the sample which is closest to mean of all
     the experiments. 
      Specify 'refType = "mean"'. 

      3. The reference is the sample which is closest to median of all
     the experiments. 
      Specify 'refType = "median"'. 

      4. The reference is the mean of all experiments in the
     'qpcrBatch' object. 
      Specify 'refType = "pseudo.mean"'. 

      5. The reference is the median of all experiments in the
     'qpcrBatch' object. 
      Specify 'refType = "pseudo.median"'. 

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

     A 'qpcrBatch' object, the 'normalized' slot is now set at TRUE. 
     The names of the rank-invariant genes used for normalization are
     stored as a vector in the 'normGenes' slot of the 'qpcrBatch'
     object returned. To retrieve the rank-invariant gene names, use
     'qpcrBatch@normGenes'.

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

     Jess Mar jess@jimmy.harvard.edu

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

     'normQpcrQuantile', 'normalize.invariantset'

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

      data(qpcrBatch.object)
      mynormRI.data <- normQpcrRankInvariant(qpcrBatch.object, 1) 
      mynormRI.data@normGenes                # retrieves names of genes in the rank-invariant set

