PLMset-class             package:affyPLM             R Documentation

_C_l_a_s_s _P_L_M_s_e_t

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

     This is a class representation for Probe level Linear Models
     fitted to Affymetrix GeneChip probe level data.

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

     Objects can be created using the function 'fitPLM'

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

     '_p_r_o_b_e._c_o_e_f_s': Object of class "matrix". Contains model
          coefficients related to probe effects

     '_s_e._p_r_o_b_e._c_o_e_f_s': Object of class "matrix". Contains standard
          error estimates for the probe coefficients  

     '_c_h_i_p._c_o_e_f_s': Object of class "matrix". Contains model
          coefficients related to chip (or chip level) effects for each
          fit.

     '_s_e._c_h_i_p._c_o_e_f_s': Object of class "matrix". Contains standard error
          estimates for the chip coefficients

     '_m_o_d_e_l._d_e_s_c_r_i_p_t_i_o_n': Object of class "character". This string
          describes the probe level model fitted.

     '_w_e_i_g_h_t_s': Object of class "matrix". Contains probe weights for
          each fit. The matrix has columns for chips and rows are
          probes

     '_p_h_e_n_o_D_a_t_a': Object of class "phenoData" This is an instance of
          class 'phenoData'  containing the patient (or case) level
          data. The columns of the pData slot of this entity represent
          variables and the rows represent patients or cases. 

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

     '_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.

     '_c_d_f_N_a_m_e': A character string giving the name of the cdfFile

     '_n_r_o_w': Object of class "numeric". Number of rows in chip

     '_n_c_o_l': Object of class "numeric". Number of cols in chip

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

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

     Class '"exprSet"', directly.

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

     _w_e_i_g_h_t_s<- 'signature(object = "PLMset")': replaces the weights 

     _w_e_i_g_h_t_s 'signature(object = "PLMset")': extracts the model fit
          weights

     _c_o_e_f_s<- 'signature(object = "PLMset")': replaces the chip coefs.  

     _c_o_e_f_s 'signature(object = "PLMset")': extracts the chip coefs. 

     _s_e 'signature(object = "PLMset")': extracts the standard error
          estimates of the chip coefs. 

     _s_e<- 'signature(object = "PLMset")': replaces the standard error
          estimates of the chip coefs. 

     _c_o_e_f_s._p_r_o_b_e 'signature(object = "PLMset")': extracts the probe
          coefs. 

     _s_e._p_r_o_b_e 'signature(object = "PLMset")': extracts the standard
          error estimates of the probe coefs.     

     _c_o_e_f_s._c_o_n_s_t 'signature(object = "PLMset")': extracts the intercept
          coefs. 

     _s_e._c_o_n_s_t 'signature(object = "PLMset")': extracts the standard
          error estimates of the intercept coefs. 

     _g_e_t_C_d_f_I_n_f_o 'signature(object = "PLMset")': retrieve the
          environment that defines the location of probes by probe set. 

     _i_m_a_g_e 'signature(x = "PLMset")': creates an image of the robust
          linear model fit weights for each sample.

     _i_n_d_e_x_P_r_o_b_e_s 'signature(object = "PLMset", which = "character")':
          returns a list with locations of the probes in each probe 
          set. The list names defines the probe set names. 'which' can
          be "pm", "mm", or "both". If "both" then perfect match
          locations are given followed by mismatch locations.

     _M_b_o_x 'signature(object = "PLMset")': gives a boxplot of M's for
          each chip. The M's are computed relative to a "median" chip.

_N_o_t_e:

     This class is better described in the vignette.

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

     B. M. Bolstad bolstad@stat.berkeley.edu

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

