pairwise.filter          package:simpleaffy          R Documentation

_F_i_l_t_e_r _p_a_i_r_w_i_s_e _c_o_m_p_a_r_i_s_o_n _s_t_a_t_i_s_t_i_c_s _b_e_t_w_e_e_n _t_w_o _e_x_p_e_r_i_m_e_n_t_a_l _g_r_o_u_p_s

_D_e_s_c_r_i_p_t_i_o_n:

     Given the results of a pairwise.comparison, filter the resulting
     gene list on expression level, PMA calls (if available), fold
     change and t-test statistic. 

     min.exp and min.exp.no allow the data to be filtered on intensity
     (where min.exp.no specifies the minimum number of arrays that must
     be above the threshold 'min.exp' to be allowed through the
     filter).

     PMA filtering is done when min.present.number is greater than 0.

     min.present.no allows arrays to be filtered by PMA call. A number
     or 'all' must be specified. If a number, then the at least this
     many arrays must be called present, if 'all', then all arrays must
     be called present. 

     present.by.group specifies whether PMA filtering is to be done on
     a per-group basis or for all arrays at once. If 'false' then the
     experiment is treated as a single group (i.e. a probeset passes
     the filter if it is called present on at least min.present.number
     arrays in the whole experiment. If 'true' then it must be called
     present on at least this many arrays in one or more groups. See
     the vignette for more details.

_U_s_a_g_e:

       pairwise.filter(object,min.exp=log2(100),min.exp.no=0,min.present.no=0,present.by.group=T,fc=1.0,tt=0.001)

_A_r_g_u_m_e_n_t_s:

  object: a 'PairComp' object 

 min.exp: Filter genes using a minimum expression cut off 

min.exp.no: A gene must have an expression intensity greater than
          'min.exp' in at least this number of chips 

min.present.no: A gene must be called present on at least this number
          of chips 

present.by.group: If true, then the probeset must be called Present on
          at least min.present.number arrays in any of the replicate
          sets used to generate the PairComp object being filtered. If
          false, then must be called present on at least min.present.no
          of the arrays in the whole experiment 

      fc: A gene must show a log2 fold change greater than this to be
          called significant 

      tt: A gene must be changing with a p-score less than this to be
          called significant 

_V_a_l_u_e:

     A 'PairComp' object filtered to contain only the genes that pass
     the specified filter parameters.

_A_u_t_h_o_r(_s):

     Crispin J Miller

_R_e_f_e_r_e_n_c_e_s:

     http://bioinformatics.picr.man.ac.uk/

_E_x_a_m_p_l_e_s:

      
       ## Not run: 
         pc <- pairwise.comparison(eset.rma,"group",c("A","P"))
         pf <- pairwise.filter(pc,tt=0.01);
       
     ## End(Not run)