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': List of objects 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 '_v_a_r_c_o_v': Object of class "list". A list of variance/covariance matrices '_r_e_s_i_d_u_a_l_S_E': Object of class "matrix". Contains residual standard error and df '_r_e_s_i_d_u_a_l_s': List of objects of class "matrix". Contains residuals from model fit (if stored) _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_r_m_v_e_c 'signature(x = "PLMset")': will return the normalization vector (if it has been stored) _r_e_s_i_d_S_E 'signature(x = "PLMset")': will return the residual SE (if it has been stored) _b_o_x_p_l_o_t 'signature(x = "PLMset")': Boxplot of Normalized Unscaled Standard Errors (NUSE) _N_U_S_E 'signature(x = "PLMset")' : Boxplot of Normalized Unscaled Standard Errors (NUSE) or NUSE values _R_L_E| 'signature(x = "PLMset")' : Relative Log Expression boxplot or values _N_o_t_e: This class is better described in the vignette. _A_u_t_h_o_r(_s): B. M. Bolstad bmb@bmbolstad.com _R_e_f_e_r_e_n_c_e_s: Bolstad, BM (2004) _Low Level Analysis of High-density Oligonucleotide Array Data: Background, Normalization and Summarization_. PhD Dissertation. University of California, Berkeley. _E_x_a_m_p_l_e_s: