AffyBatch-class package:affy R Documentation _C_l_a_s_s _A_f_f_y_B_a_t_c_h _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 from multiple arrays of the same 'CDF' type. It extends 'exprSet-class'. _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 'read.affybatch' or the wrapper 'ReadAffy'. _S_l_o_t_s: '_c_d_f_N_a_m_e': Object of class '"character"' representing the name of 'CDF' file associated with the arrays in the 'AffyBatch'. '_n_r_o_w': Object of class '"numeric"' representing the physical number of rows in the arrays. '_n_c_o_l': Object of class '"numeric"' representing the physical number of columns in the arrays. '_e_x_p_r_s': Object of class "matrix" inherited from 'exprSet'. The matrix contains one probe per row and one chip per column. '_s_e._e_x_p_r_s': Object of class "matrix" inherited from 'exprSet'. '_p_h_e_n_o_D_a_t_a': Object of class "phenoData" inherited from 'exprSet'. '_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. '_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: _c_d_f_N_a_m_e 'signature(object = "AffyBatch")': Obtains the cdfName slot. _p_m<- 'signature(object = "AffyBatch")': replaces the perfect match intensities _p_m 'signature(object = "AffyBatch")': extracts the pm intensities. _m_m<- 'signature(object = "AffyBatch")': replaces the mismatch intensities. _m_m 'signature(object = "AffyBatch")': extracts the mm intensities. _p_r_o_b_e_s 'signature(object = "AffyBatch", which)': extract the perfect match or mismatch probe intensities. Uses which can be "pm" and "mm". [<- 'signature(x = "AffyBatch")': replaces subsets. [ 'signature(x = "AffyBatch")': subsets by array. [[ 'signature(x = "AffyBatch")': extracts each array as an 'Cel' instance. _b_o_x_p_l_o_t 'signature(x = "AffyBatch")': creates a 'boxplots of log base 2 intensities. ' _h_i_s_t 'signature(x = "AffyBatch")': creates a plot showing all the histograms of the pm,mm or both data. See 'plot.density' _c_o_m_p_u_t_e_E_x_p_r_S_e_t 'signature(x = "AffyBatch", summary.method = "character")': For each probe set computes an expression value using 'summary.method'. _g_e_n_e_N_a_m_e_s 'signature(object = "AffyBatch")': return the probe set names also referred to as the Affymetrix IDs. Notice that one can not assign geneNames. You must do this by changing the cdfenvs. _g_e_t_C_d_f_I_n_f_o 'signature(object = "AffyBatch")': retrieve the environment that defines the location of probes by probe set. _i_m_a_g_e 'signature(x = "AffyBatch")': creates an image for each sample. _i_n_d_e_x_P_r_o_b_e_s 'signature(object = "AffyBatch", which = "character")': returns a list with locations of the probes in each probe set. The affyID corresponding to the probe set to retrieve can be specified in an optional parameter 'genenames'. By default, all the affyIDs are retrieved. The names of the elements in the list returned are the affyIDs. 'which' can be "pm", "mm", or "both". If "both" then perfect match locations are given followed by mismatch locations. 'signature(object = "AffyBatch", which = "missing")' (i.e., calling 'indexProbes' without a "which" argument) is the same as setting "which" to "pm". _i_n_t_e_n_s_i_t_y<- 'signature(object = "AffyBatch")': a replacement method for the 'exprs' slot, i.e. the intensities. _i_n_t_e_n_s_i_t_y 'signature(object = "AffyBatch")': extract the 'exprs' slot, i.e. the intensities. _l_e_n_g_t_h 'signature(x = "AffyBatch")': returns the number of samples. _p_m_i_n_d_e_x 'signature(object = "AffyBatch")': return the location of perfect matches in the intensity matrix. _m_m_i_n_d_e_x 'signature(object = "AffyBatch")': return the location of the mismatch intensities. _n_c_o_l 'signature(x = "AffyBatch")': An accessor function for 'ncol'. _n_r_o_w 'signature(x = "AffyBatch")': an accessor function for 'nrow'. _n_o_r_m_a_l_i_z_e 'signature(object = "AffyBatch")': a method to 'normalize'. The method accepts an argument 'method'. The default methods is specified in package options (see the main vignette). _n_o_r_m_a_l_i_z_e._m_e_t_h_o_d_s 'signature(object = "AffyBatch")': returns the normalization methods defined for this class. See 'normalize'. _p_r_o_b_e_N_a_m_e_s 'signature(object = "AffyBatch")': returns the probe set associated with each row of the intensity matrix. _p_r_o_b_e_s_e_t 'signature(object = "AffyBatch",genenames=NULL, locations=NULL)': Extracts 'ProbeSet' objects related to the probe sets given in genenames. If an alternative set of locations defining pms and mms a list with those locations should be passed via the 'locations' argument. _b_g._c_o_r_r_e_c_t 'signature(object = "AffyBatch", method="character")' applies background correction methods defined by method. _N_o_t_e: This class is better described in the vignette. _S_e_e _A_l_s_o: related methods 'merge.AffyBatch', 'pairs.AffyBatch', and related classes 'Cel', 'Cdf' and 'exprSet-class' _E_x_a_m_p_l_e_s: ## load example data(affybatch.example) ## nice print print(affybatch.example) pm(affybatch.example)[1:5,] mm(affybatch.example)[1:5,] ## get indexes for the PM probes for the affyID "A28102_at" mypmindex <- pmindex(affybatch.example,"A28102_at") ## same operation using the primitive mypmindex <- indexProbes(affybatch.example, which="pm", genenames="A28102_at")[[1]] ## get the probe intensities from the index intensity(affybatch.example)[mypmindex, ] ## load bigger example (try 'help(Dilution)' ) data(affybatch.example) description(affybatch.example) ##we can also use the methods of exprSet sampleNames(affybatch.example) abstract(affybatch.example)