exprReslt-class             package:puma             R Documentation

_C_l_a_s_s _e_x_p_r_R_e_s_l_t

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

     This is a class representation for Affymetrix GeneChip probe level
     data.  The main component are the intensities, estimated
     expression levels and the confidence  of expression levels from
     multiple arrays  of the same 'CDF' type. In extends
     'ExpressionSet'.

_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("exprReslt",
     ...)'.

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


     '_p_r_c_f_i_v_e': Object of class "matrix" representing the 5 percentile
          of the  observed expression levels. This is a matrix with
          columns representing patients or cases and  rows representing
          genes. 

     '_p_r_c_t_w_f_i_v_e': Object of class "matrix" representing the 25
          percentile of the  observed expression levels. This is a
          matrix with columns representing patients or cases and  rows
          representing genes.

     '_p_r_c_f_i_f_t_y': Object of class "matrix" representing the 50
          percentile of the  observed expression levels. This is a
          matrix with columns representing patients or cases and  rows
          representing genes.

     '_p_r_c_s_e_v_f_i_v_e': Object of class "matrix" representing the 75
          percentile of the  observed expression levels. This is a
          matrix with columns representing patients or cases and  rows
          representing genes.

     '_p_r_c_n_i_n_f_i_v_e': Object of class "matrix" representing the 95
          percentile of the  observed expression levels. This is a
          matrix with columns representing patients or cases and  rows
          representing genes.

     '_e_x_p_r_s': Object of class "matrix" representing the  observed
          expression levels. This is a matrix with columns representing
          patients or cases and  rows representing genes. 

     '_s_e._e_x_p_r_s': Object of class "matrix" representing the standard
          deviation of the  observed expression levels. This is a
          matrix with columns representing patients or cases and  rows
          representing genes.

     '_p_h_e_n_o_D_a_t_a': Object of class "phenoData" inherited from
          'ExpressionSet'.

     '_d_e_s_c_r_i_p_t_i_o_n': Object of class "MIAME". For compatibility with
          previous version of this class description can also be a
          "character". The class 'characterOrMIAME' has been defined
          just for this.

     '_a_n_n_o_t_a_t_i_o_n': A character string identifying the annotation that
          may be used for the 'ExpressionSet' instance.

     '_n_o_t_e_s': Object of class "character" Vector of explanatory text 

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

     Class '"ExpressionSet"', directly.

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


     _s_e._e_x_p_r_s 'signature(object = "exprReslt")': obtains the standard
          error of the estimated  expression levels. 

     _s_e._e_x_p_r_s<- 'signature(object = "exprReslt")': replaces the
          standard error of the estimated  expression levels. 

     _p_r_c_f_i_f_t_y 'signature(object = "exprReslt")': obtains the 50
          percentile of the estimated  expression levels. 

     _p_r_c_f_i_f_t_y<- 'signature(object = "exprReslt")': replaces the 50
          percentile of the estimated  expression levels. 

     _p_r_c_f_i_v_e 'signature(object = "exprReslt")': obtains the 5
          percentile of the estimated  expression levels.  

     _p_r_c_f_i_v_e<- 'signature(object = "exprReslt")': replaces the 5
          percentile of the estimated  expression levels.  

     _p_r_c_n_i_n_f_i_v_e 'signature(object = "exprReslt")': obtains the 95
          percentile of the estimated  expression levels.  

     _p_r_c_n_i_n_f_i_v_e<- 'signature(object = "exprReslt")': replaces the 95
          percentile of the estimated  expression levels.  

     _p_r_c_s_e_v_f_i_v_e 'signature(object = "exprReslt")': obtains the 75
          percentile of the estimated  expression levels.  

     _p_r_c_s_e_v_f_i_v_e<- 'signature(object = "exprReslt")': replaces the 75
          percentile of the estimated  expression levels.  

     _p_r_c_t_w_f_i_v_e 'signature(object = "exprReslt")': obtains the 25
          percentile of the estimated  expression levels.  

     _p_r_c_t_w_f_i_v_e<- 'signature(object = "exprReslt")': replaces the 25
          percentile of the estimated  expression levels.  

     _s_h_o_w 'signature(object = "exprReslt")': renders information about
          the exprReslt in a concise  way on stdout. 

     _w_r_i_t_e._r_e_s_l_t_s 'signature(x = "exprReslt")': writes the expression
          levels and related confidences to files. It takes the same
          arguments as 'write.table'. The argument "file" does not need
          to set any  extension. The different file marks and extension
          "csv" will be added automatically. The default file name is
          "tmp".  In the final results, expression levels are in the
          file "tmp_exprs.csv", standard deviations in  "tmp_se.csv", 5
          percentiles in "tmp_prctile5.csv", likewise, 25, 50, 75 and
          95 percentiles in "tmp_prctile25.csv",  "tmp_prctile50.csv",
          "tmp_prctile75.csv" and "tmp_prctile95.csv" respectively. 

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

     Xuejun Liu, Magnus Rattray, Marta Milo, Neil D. Lawrence, Richard
     D. Pearson

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

     Related method 'mmgmos' and related class 'ExpressionSet'.

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

     ## load example data from package Affy
     data(affybatch.example)

     ## use method mmgmos to calculate the expressiong levels and related confidences 
     ## of the measures for affybatch.example
     eset<-mmgmos(affybatch.example)

     ## save the expression resluts into files
     write.reslts(eset, file="example")

