applera               package:applera               R Documentation

_C_l_a_s_s "_a_p_p_l_e_r_a" ~~~

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

     This is class representation for Applera Microarray Data.

_O_b_j_e_c_t_s _f_r_o_m _t_h_e _C_l_a_s_s:

     Objects can be created by calls of the form 'new("applera",
     Organism= ..., #Object of class character,  Geneid= ..., #Object
     of class vector,  Signal= ..., #Object of class exprSet,  Sdev=
     ..., #Object of class exprSet,  Cv= ..., #Object of class exprSet,
      Sn= ..., #Object of class exprSet, Flags= ..., #Object of class
     exprSet,  Ctrl= ..., #Object of class list.)'.

_S_l_o_t_s:

     '_O_r_g_a_n_i_s_m': Object of class '"character"' A string describing the
          organism implemented in the array: "Hs" for human, "Mm" for
          mouse, "Rn" for rat. 

     '_G_e_n_e_i_d': Object of class '"character"' A vector of primary Ids
          associated to spotted probes. 

     '_S_i_g_n_a_l': Object of class '"exprSet"' it contains all the log2
          chemiolominescence (CL) expression signals. The CL signal is
          normalized by the fluorescence (FL) signal over the feature
          integration aperture. See AB1700 manual. 

     '_S_d_e_v': Object of class '"exprSet"' An estimated measurement
          uncertainty of Normalized Signal. See ABI1700 manual. 

     '_C_v': Object of class '"exprSet"' The fraction of uncertainty in
          the signal. Cv indicates the predicted spread of feature
          signal. See AB1700 manual. 

     '_S_n': Object of class '"exprSet"' The ratio Signal/Sdev. S/N
          expresses the confidence of feature dectability. See AB1700
          manual. 

     '_F_l_a_g_s': Object of class '"exprSet"' A numeric code that
          identifies conditions for each feature. It allows to
          eliminate possibily problematic data. Features with flags
          greater than 100 might have quality issues. See AB1700
          manual. 

     '_C_t_r_l': Object of class '"list"' All controls spots values for
          Signal, Sdev, Cv, Sn and Flags. See ABI1700 manual. 

     '_e_x_p_r_s': Object of class '"exprMatrix"' All data in slots Signal,
          Sdev, Cv, Sn and Flags are represented as exprSet object 

     '_s_e._e_x_p_r_s': Object of class '"exprMatrix"' Not used 

     '_p_h_e_n_o_D_a_t_a': Object of class '"phenoData"' All data in slots
          Signal, Sdev, Cv, Sn and Flags contain the phenoData used to
          build the applera object

     '_d_e_s_c_r_i_p_t_i_o_n': Object of class '"characterORMIAME"' Not used 

     '_a_n_n_o_t_a_t_i_o_n': Object of class '"character"' Not used 

     '_n_o_t_e_s': Object of class '"character"' Not used 

_E_x_t_e_n_d_s:

     Class '"exprSet"', directly.

_M_e_t_h_o_d_s:

     _a_p_F_i_l_t_e_r 'signature(apObj = "applera")': Function to filter an
          appleraSet by Sn or Flags

     _b_o_x_p_l_o_t 'signature(x = "applera")': Boxplot representation of
          slots data 

     _c_t_r_l 'signature(object = "applera")': Function returning the list
          associated to the Ctrl slot 

     _c_v_A_p 'signature(object = "applera")': Function returning the
          exprSet associated to the Cv slot 

     _f_l_a_g_s 'signature(object = "applera")': Function returning the
          exprSet associated to the Flags slot 

     _g_e_n_e_i_d 'signature(object = "applera")': Function returning the
          Geneid slot 

     _h_i_s_t 'signature(x = "applera")': Density distributions of slots
          data 

     _i_q_r_F_i_l_t_e_r 'signature(apObj = "applera")': Function to filter an
          appleraSet, given a  specific IQR values. 

     _m_v_a_A_p 'signature(apObj = "applera")': mva.pairs representation of
          Signal slot data 

     _n_o_r_m_L_o_e_s_s 'signature(apObj = "applera")': Function to normalize an
          appleraSet using the normalize.loess function of the affy
          package 

     _n_o_r_m_Q_u_a_n_t_i_l_e 'signature(apObj = "applera")': Function to normalize
          an appleraSet using the normalize.quantile function of the
          affy package 

     _o_r_g_a_n_i_s_m 'signature(object = "applera")': Function returning the
          Organism slot 

     _s_d_e_v 'signature(object = "applera")': Function returning the
          exprSet associated to the Sdev slot 

     _s_h_o_w 'signature(object = "applera")': Renders information about
          the appleraSet in a concise way on stdout 

     _s_i_g_n_a_l 'signature(object = "applera")': Function returning the
          exprSet associated to the Signal slot 

     _s_n 'signature(object = "applera")': Function returning the exprSet
          associated to the Sn slot 

     _s_u_b_E_x_p 'signature(apObj = "applera")': Function to subset an
          appleraSet given a vector of sampleNames 

     _s_u_b_G_e_n_e_s 'signature(apObj = "applera")': Function to subset an
          appleraSet given a vector of geneNames 

_N_o_t_e:

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

     Raffaele A. Calogero <raffaele.calogero@unito.it>; Francesca
     Cordero <fcordero@di.unito.it>

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

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

     'readAp'

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

