read.celfile.probeintensity.matrices package:affyio R Documentation _R_e_a_d _P_M _o_r _M_M _f_r_o_m _C_E_L _f_i_l_e _i_n_t_o _m_a_t_r_i_c_e_s _D_e_s_c_r_i_p_t_i_o_n: This function reads PM, MM or both types of intensities into matrices. These matrices have all the probes for a probeset in adjacent rows _U_s_a_g_e: read.celfile.probeintensity.matrices(filenames, cdfInfo, rm.mask=FALSE, rm.outliers=FALSE, rm.extra=FALSE, verbose=FALSE, which= c("pm","mm","both")) _A_r_g_u_m_e_n_t_s: filenames: a 'list' of filenames cdfInfo: a list with items giving PM and MM locations for desired probesets. In same structure as returned by 'make.cdf.package' rm.mask: a 'logical'. Return these probes as NA if there are in the [MASK] section of the CEL file rm.outliers: a 'logical'. Return these probes as NA if there are in the [OUTLIERS] section of the CEL file rm.extra: a 'logical'. Return these probes as NA if there are in the [OUTLIERS] section of the CEL file verbose: a 'logical'. When true the parsing routine prints more information, typically useful for debugging. which: a string specifing which probe type to return _V_a_l_u_e: returns a 'list' of 'matrix' items. One matrix contains PM probe intensities, with probes in rows and arrays in columns _A_u_t_h_o_r(_s): B. M. Bolstad