LiWongRank             package:RNAither             R Documentation

_L_i _W_o_n_g _r_a_n_k / _i_n_v_a_r_i_a_n_t _p_r_o_b_e_s_e_t _n_o_r_m_a_l_i_z_a_t_i_o_n

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

     Performs a Li Wong rank / invariant probeset normalization (see
     References).

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

     LiWongRank(header, dataset, listOfArgs)

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

  header: the header of a dataset file generated with
          'generateDatasetFile' 

 dataset: an R data frame generated with 'generateDatasetFile' 

listOfArgs: a list containing:

          - a character string specifying the column whose values will
          be used for normalization

          - a character string specifying the name of the dataset
          column to be used for the computation of the siRNA/gene ranks            

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

     For each plate type/layout in each experiment, generates a ranked
     list of siRNAs according to their intensity values. Only siRNAs
     occuring only once on the plate are allowed in the list. The
     normalization is performed only if all plate types have a maximum
     of 20 

     For each "unique" siRNA on a plate type, the variance of its ranks
     across plates is computed. A histogram of variances is plotted and
     allows the user to choose a threshold. A list of siRNAs with rank
     variances under the given threshold is then returned for each
     plate type so that the user can choose an siRNA to normalize the
     plate with.

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

     Returns a list containing: 

 header : the new header (with an added entry about the normalization
          procedure in the comments)

dataset : the new dataset with normalized values. The old values are
          saved in an extra column with the suffix ".old"

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

     C. Li and WH Wong. Model-based analysis of oligonucleotide arrays:
     model validation, design issues and standard error application.
     Genome Biol, 2(8):research0032.1-0032.11, 2001.

     E. Schadt, C. Li, B. Ellis, and WH Wong. Feature Extraction and
     Normalization Algorithms for High-Density Oligonucleotide Gene
     Expression Array Data. J Cell Biochem Suppl, 37:120-125, 2001.

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

     data(exampleHeader, package="RNAither")
     data(exampleDataset, package="RNAither")

     normres <- LiWongRank(header, dataset, list("SigIntensity", "GeneName"))
     0.5
     3
     2
     3
     newheader=normres[[1]]
     newdataset=normres[[2]]

