justPlier               package:plier               R Documentation

_I_m_p_l_e_m_e_n_t_s _t_h_e _P_L_I_E_R _a_l_g_o_r_i_t_h_m

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

     Provides a wrapper around Affymetrix's API to provide an
     implementation of the PLIER alogrimth

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

     justPlier(eset=ReadAffy(),replicate=1:length(eset),get.affinities=FALSE,normalize=F,norm.type="together",augmentation=0.1,defaultaffinity=1.0,defaultconcentration=1.0,attenuation=0.005,seaconvergence=0.000001,seaiteration=3000,gmcutoff=0.15,probepenalty=0.001,concpenalty=0.000001,usemm=TRUE,usemodel=FALSE,fitaffinity=T,plierconvergence=0.000001,plieriteration=3000,dropmax=3.0,lambdalimit=0.01,optimization=0)

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

    eset: An AffyBatch object containing the raw data 

replicate: A factor containing the replicate structure to use for
          grouping samples 

get.affinities: If TRUE, then return affinities in the preprocessing
          slot of the exprSet object 

normalize: If TRUE then apply quantile normalization to the probes
          before generating expression calls 

norm.type: Can be 'separate', 'pmonly', 'mmonly' or 'together' 

augmentation: Model parameter 

defaultaffinity: Model parameter 

defaultconcentration: Model parameter 

attenuation: Model parameter 

seaconvergence: Model parameter 

seaiteration: Model parameter 

gmcutoff: Model parameter 

probepenalty: Model parameter 

concpenalty: Model parameter 

   usemm: Model parameter 

usemodel: Model parameter 

fitaffinity: Model parameter 

plierconvergence: Model parameter 

plieriteration: Model parameter 

 dropmax: Model parameter 

lambdalimit: Model parameter 

optimization: Model parameter 

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

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

     An Expression set containing PLIER generated expression calls

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

     Crispin J Miller (wrapper), Earl Hubbell (algorithm)

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

     <URL: bioinf.picr.man.ac.uk> <URL: www.affymetrix.com>

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

     normalize.AffyBatch.quantiles

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

