Filter              package:AffyExpress              R Documentation

_f_i_l_t_e_r _a_n '_E_x_p_r_e_s_s_i_o_n_S_e_t' _u_s_i_n_g _d_i_f_f_e_r_e_n_t _m_e_t_h_o_d_s

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

     Create a filtered 'ExpressionSet' based on background, range, or
     interquartile range

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

       Filter(object, numChip=1, bg=0, range=0, iqrPct=0)

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

  object: an 'ExpressionSet'

 numChip: number of chips.  If you would like to filter the
          'ExpressionSet' based on at least 3 chips greater than 1
          (bg=1), then set numChip = 3

      bg: background value. If you would like to filter the
          'ExpressionSet' based on at least 3 chips greater than 1,
          then set bg=1

   range: range = max value - min value of each gene

  iqrPct: interquartile percentage.

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

     There are three filtering methods.  The User can use either one,
     two, or three. 1.  At least a certain number of chips (numChip)
     are greater than a given  background (bg). 2.  The range of the
     gene have to be greater than a given value (range). 3.  Calulating
     the interquatile range (IQR) of each gene to create an IQR vector.
     Based on the given percentage (e.g. iqrPct=0.2), find the
     corresponding percentile.  If IQR is less than percentile, the
     gene will be filtered.

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

     a filtered 'ExpressionSet'

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

     Xiwei Wu xwu@coh.org, Xuejun Arthur Li xueli@coh.org

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

     data(testData)
     normaldata<-pre.process("rma",testData)

     ##At least one chip is greater than 4
     filtered.1<-Filter(normaldata, numChip=1, bg=4)  

     ##At least one chip is greater than 4 and range >0.5
     filtered.2<-Filter(normaldata, numChip=1, bg=4, range=0.5)  

     ##range >0.5 and IQR > 20percentile
     filtered.3<-Filter(normaldata, range=0.5, iqrPct=0.2)  

