generateExprSet-method         package:affy         R Documentation

_g_e_n_e_r_a_t_e _a _s_e_t _o_f _e_x_p_r_e_s_s_i_o_n _v_a_l_u_e_s

_D_e_s_c_r_i_p_t_i_o_n:

     Generate a set of expression values from the probe pair
     information. The set of expression is returned as an
     'ExpressionSet' object.

_U_s_a_g_e:

       computeExprSet(x, pmcorrect.method, summary.method, ...)

       generateExprSet.methods

_A_r_g_u_m_e_n_t_s:

       x: a 'AffyBatch' holding the probe level informations to
          generate the expression values.

pmcorrect.method: the method used to correct PM values (see section
          'details').

summary.method: the method used to generate the expression value (see
          section 'details').

     ...: any of the options of the normalization you would like to
          modify

_D_e_t_a_i_l_s:

     An extra argument 'ids=' can be passed. It must be a vector of
     affids. The expression values will only be computed and returned
     for these affyids.

     The different methods available through this mecanism can be
     accessed by calling the method 'generateExprSet.methods' with an
     object of call 'Cel.container' as an argument.

     In the Affymetrix design, _MM_ probes were included to measure the
     noise (or background signal). The original algorithm for
     background correction was to subtract the _MM_ signal to the _PM_
     signal. The methods currently inclluded in the package are
     "bg.correct.subtractmm", "bg.correct.pmonly" and
     "bg.correct.adjust".

_S_e_e _A_l_s_o:

     method 'generateExprSet' of the class 'AffyBatch'
      'expresso'

_E_x_a_m_p_l_e_s:

      data(affybatch.example)

      ids <- c( "A28102_at","AB000114_at")
       
       eset <- computeExprSet(affybatch.example, pmcorrect.method="pmonly",
     summary.method="avgdiff", ids=ids)

