optFilter              package:applera              R Documentation

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

     The function 'optFilter'  optimizes filtering procedure for two
     classes experiment (e.g. untreated vs treated) using limma linear
     model analysis. The function needs an applera object, the
     covariate name allowing the separation of the data in two groups,
     a S/N value (see definition of Sn in applera-class help), a set of
     p conditions indicating the minimum percentage of experiments 
     characterized by a specific sn.value, a range of IQR values (see
     iqrFilter definition in applera-class help). When an applera
     object, characterized by a phenodata covariate allowing the
     separation in two groups, is passed to the function the set of
     user-defined filtering combinations based on S/N ratio and IQR
     values are generated and the filtered data stes are passed to the
     limma package. The output of the function is  the filtering
     combination that will produce the higher number of differentially
     expressed genes. The rationale of this approach is to reduce as
     much as possible the non-significative genes and to limit the
     number of genes passed to statistical tests. However, very
     stringent filtering might eliminate also many significative genes.
     This function try to find the best compromise to generate a
     filtered set of genes in which are removed low quality features
     (sn filter, see the snFilter defition in the applera-class help)
     and unchanged genes (iqrFilter will remove all genes with limited
     variation within the experiments)

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

     optFilter(apObj, covariate , sn.value=3, p=c(1, 0.75, 0.5, 0.25), iqr.value=c(0.5, 0.25))

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

   apObj: an applera object

covariate: a phenodata covariate allowing the separation of the
          experiments in two groups

sn.value: indicates the threshold for S/N ratio to be considered
          significant. 3 indicate a 99.9 confidence that the signal is
          different from bg

       p: indicates the percentage of experiments characterized by a
          specific sn value

iqr.value: indicates the IQR threshold 

_V_a_l_u_e:

     An object of class "applera".

_A_u_t_h_o_r(_s):

     Raffaele A. Calogero <raffaele.calogero@unito.it>; Francesca
     cordero <fcordero@di.unito.it>

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

     'applera-class' for the class of the return value.

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

     #tmp.1 <- optFilter(test, "wk" , sn.value=3, p=c(1, 0.75, 0.5, 0.25), iqr.value=c(0.5, 0.25))

