1. Dictionary           package:affxparser           R Documentation

_1. _D_i_c_t_i_o_n_a_r_y

_D_e_s_c_r_i_p_t_i_o_n:

     This part describes non-obvious terms used in this package.

     _a_f_f_x_p_a_r_s_e_r The name of this package.

     _A_P_I Application program interface, which describes the functional
          interface of underlying methods.

     _b_l_o_c_k (aka group).

     _B_P_M_A_P A file format containing information related to the design
          of the tiling arrays.

     _C_a_l_v_i_n A special binary file format.

     _C_D_F A file format: chip definition file.

     _C_E_L A file format: cell intensity file.

     _c_e_l_l (aka feature) A probe.

     _c_e_l_l _i_n_d_e_x An integer that identifies a probe uniquely.

     _c_h_i_p An array.

     _c_h_i_p _t_y_p_e An identifier specifying a chip design uniquely, e.g.
          '"Mapping50K_Xba240"'.

     _D_A_T A file format: contains pixel intensity values collected from
          an Affymetrix GeneArray scanner.

     _f_e_a_t_u_r_e A probe.

     _F_u_s_i_o_n _S_D_K Open-source sofware development kit (SDK) provided by
          Affymetrix to access their data files.

     _g_r_o_u_p (aka block) Defines a unique subset of the cells in a unit.
          Expression arrays typically only have one group per unit,
          whereas SNP arrays have either two or four groups per unit,
          one for each of the two allele times possibly repeated for
          both strands.

     _M_M Mismatch-match, e.g. MM probe.

     _T_P_M_A_P A file format storing the relationship between (PM,MM) pairs
          (or PM probes) and positions on a set of sequences.

     _Q_C Quality control, e.g. QC probes and QC probe sets.

     _u_n_i_t A probeset.

     _X_D_A A file format, aka as the binary file format.

_A_u_t_h_o_r(_s):

     Henrik Bengtsson (<URL: http://www.braju.com/R/>)

