mas5                  package:affy                  R Documentation

_M_A_S _5._0 _e_x_p_r_e_s_s_i_o_n _m_e_a_s_u_r_e

_D_e_s_c_r_i_p_t_i_o_n:

     This function converts an instance of 'AffyBatch' into an instance
     of 'ExpressionSet' using our implementation of Affymetrix's MAS
     5.0 expression measure.

_U_s_a_g_e:

     mas5(object, normalize = TRUE, sc = 500, analysis = "absolute", ...)

_A_r_g_u_m_e_n_t_s:

  object: an instance of 'AffyBatch'

normalize: logical. If 'TRUE' scale normalization is used after we
          obtain an instance of 'ExpressionSet'

      sc: Value at which all arrays will be scaled to.

analysis: should we do absolute or comparison analysis, although
          "comparison" is still not implemented.

     ...: other arguments to be passed to 'expresso'.

_D_e_t_a_i_l_s:

     This function is a wrapper for  'expresso' and
     'affy.scalevalue.exprSet'.

_V_a_l_u_e:

     'ExpressionSet' 

     The methods used by this function were implemented based upon
     available documentation. In particular a useful reference is
     Statistical Algorithms Description Document by Affymetrix. Our
     implementation is based on what is written in the documentation
     and as you might appreciate there are places where the
     documentation is less than clear. This function does not give
     exactly the same results. All source code of our implementation is
     available. You are free to read it and suggest fixes. 

     For more information visit this URL:
     http://stat-www.berkeley.edu/users/bolstad/

_S_e_e _A_l_s_o:

     'expresso','affy.scalevalue.exprSet'

_E_x_a_m_p_l_e_s:

     if (require(affydata)) {
       data(Dilution)
       eset <- mas5(Dilution)
     }

