expresso                package:affy                R Documentation

_F_r_o_m _r_a_w _p_r_o_b_e _i_n_t_e_n_s_i_t_i_e_s _t_o _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:

     Goes from raw probe intensities to expression values

_U_s_a_g_e:

     expresso(
             afbatch,
         # background correction
             bg.correct = TRUE,
             bgcorrect.method = NULL,
             bgcorrect.param = list(),
         # normalize
             normalize = TRUE,
             normalize.method = NULL,
             normalize.param = list(),
         # pm correction
             pmcorrect.method = NULL,
             pmcorrect.param = list(),
         # expression values
             summary.method = NULL,
             summary.param = list(),
             summary.subset = NULL,
         # misc.
             verbose = TRUE,
             widget = FALSE)

_A_r_g_u_m_e_n_t_s:

 afbatch: An 'AffyBatch' object 

bg.correct: a boolean to express whether background correction is
          wanted or not.

bgcorrect.method: the name of the background adjustment method

bgcorrect.param: a list of parameters for bgcorrect.method (if
          needed/wanted)

normalize: normalization step wished or not.

normalize.method: the normalization method to use

normalize.param: a list of parameters to be passed to the normalization
          method (if wanted).

pmcorrect.method: the name of the PM adjustement method

pmcorrect.param: a list of parameters for pmcorrect.method (if
          needed/wanted)

summary.method: the method used for the computation of expression
          values

summary.param: a list of parameters to be passed to the
          'summary.method' (if wanted).

summary.subset: a list of 'affyids'. If 'NULL', a expression summary
          value is computed for everything on the chip.

 verbose: logical value. If 'TRUE' it writes out some messages.

  widget: a boolean to specify the use of widgets (the package tkWidget
          is required).

_D_e_t_a_i_l_s:

     Some arguments can be left to 'NULL' if the 'widget=TRUE'. In this
     case, a widget pops up and let the user choose with the mouse. The
     arguments are: 'AffyBatch', 'bgcorrect.method',
     'normalize.method', 'pmcorrect.method' and 'summary.method'.

     For the mas 5.0 and 4.0 methods ones need to normalize after
     obtaining expression. The function 'affy.scalevalue.exprSet' does
     this.

     For the Li and Wong summary method notice you will not get the
     same results as you would get with dChip. dChip is not open source
     so it is not easy to reproduce.  Notice also that this iterative
     algorithm will not always converge. If you run the algorithm on
     thousands of probes expect some non-convergence warnings. These
     are more likely when few arrays are used. We recommend using this
     method only if you have 10 or more arrays. Please refer to the
     'fit.li.wong' help page for more details.

_V_a_l_u_e:

     An object of class 'ExpressionSet', with an attribute
     'pps.warnings' as returned by the method 'computeExprSet'.

_S_e_e _A_l_s_o:

     'AffyBatch'

_E_x_a_m_p_l_e_s:

     if (require(affydata)) {
       data(Dilution)

       eset <- expresso(Dilution, bgcorrect.method="rma",
                        normalize.method="constant",pmcorrect.method="pmonly",
                        summary.method="avgdiff")

       ##to see options available for bg correction type:
       bgcorrect.methods()
     }

