NormalizeProbes             package:rMAT             R Documentation

_N_o_r_m_a_l_i_z_e _t_i_l_i_n_g _a_r_r_a_y _d_a_t_a _u_s_i_n_g _s_e_q_u_e_n_c_e _i_n_f_o_r_m_a_t_i_o_n

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

     This function is used to normalize tiling array data using
     sequence information. Users can chose between two different
     normalization methods. Please refer to the arguments section
     below.

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

     ScSetNorm<-NormalizeProbes(tilingSet, method="MAT",robust=FALSE, all=FALSE, standard=TRUE, verbose=FALSE)
                                                     

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

tilingSet: This object contains an ExpressionSet and has the following
          additional slots

  method: The normalization method to be used. User can choose from
          "MAT", or "PairBinned". As an upgrade to MAT, the Pair option
          also takes into account of the interaction between adjacent
          pairs along the probe as covariates for linear regression. 

  robust: A logical value. If TRUE, reweighted least-squares estimates
          are computed.

     all: A logical value. If not using all probes to compute (for
          faster computation and memory efficiency) the regression
          parameters, then use the minimum of 300,000 or number of
          probes, whichever is less.

 verbose: A logical value. If verbose is TRUE, progress information
          would be displayed.

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

     For the original rMAT normalization: method is set to be rMAT in
     string, robust is set to be false, copyNumber is set to be your
     copy number's vector, rMATScaling is set to be true, and
     logTransform is set to be true for untransformed data. The output
     can be saved as BAR file if the BAR argument specifies a filename,
     or as a parsed BAR file if argument output specifies a filename. 

     For more details on normalization, please refer to the following
     paper: Johnson et al. Model-based analysis of tiling-arrays for
     ChIP-chip. Proc Natl Acad Sci USA (2006) vol. 103 (33) pp.
     12457-62

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

     The matrix of normalized expression values.

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

     Charles Cheung, cykc@interchange.ubc.ca and Raphael Gottardo,
     raphael.gottardo@ircm.qc.ca Arnaud Droit, arnaud.droit@ircm.qc.ca

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

     'PairInMatrix()' for generating neighbouring pair-codes from
     sequences and 'affyTile' for information about the package.

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

     ####################################################
     #The data are in inst/doc folder in rMAT package.
     ####################################################


     pwd<-"" #INPUT FILES- BPMAP, ARRAYS, etc.
     path<- system.file("doc/Sc03b_MR_v04_10000.bpmap",package="rMAT")

     bpmapFile<-paste(pwd,path,sep="")

     pathCEL<- system.file("doc/Swr1WTIP_Short.CEL",package="rMAT")
     arrayFile<-paste(pwd,c(pathCEL),sep="")

     # Show the all the different sequences
     ReadBPMAPAllSeqHeader(bpmapFile)

     # create a tiling Set from the corresponding data
     # This will only grep the sequences with Sc

     ScSet<-BPMAPCelParser(bpmapFile, arrayFile, verbose=FALSE,groupName="Sc") 
     ScSetNorm<-NormalizeProbes(ScSet, method="MAT",robust=FALSE, all=FALSE, standard=TRUE, verbose=FALSE)
        

