sFiltertBH                package:CLL                R Documentation

_B_o_o_l_e_a_n _v_a_l_u_e_s _f_o_r _s_p_e_c_i_f_i_c _f_i_l_t_e_r_i_n_g _b_a_s_e_d _o_n _t_h_e _t-_t_e_s_t

_D_e_s_c_r_i_p_t_i_o_n:

     sFiltert is a named vector of booleans indicating whether a gene
     passed the specific and non-specific filtering steps.  The
     nonspecific filtering step was described in the nsFilter man page.
      The specific filtering was to perform row t-tests, then perform
     p-value adjustment using the Benjamini & Hochberg method (using
     the mt.rawp2adjp function in the multtest package with the "BH"
     procedure), and finally include the gene if its adjusted p-value
     was less than 0.35.  So to have a TRUE value in sFiltertBH, the
     gene must have an IQR greater than or equal to the median IQR and
     must have a BH adjusted p-value less than 0.35. 

     A TRUE value indicates that the gene passed the filtering step and
     should be included in further analysis.

_U_s_a_g_e:

     data(sFiltert)

_F_o_r_m_a_t:

     A named vector of logicals.  The names correspond to the
     Affymetrix identifiers and the values are booleans indicating
     whether the gene passed the nonspecific and specific filtering
     (based on adjusted t-test p-values).

_S_o_u_r_c_e:

     The CLL microarray data came from  Dr. Sabina Chiaretti at
     Division of Hematology, Department of Cellular Biotechnologies and
     Hematology, University La Sapienza, Rome, Italy and Dr. Jerome
     Ritz at Department of Medicine, Brigham and Women's Hospital,
     Harvard Medical School, Boston, Massachusetts.

_E_x_a_m_p_l_e_s:

     data(sFiltertBH)
     data(sCLLex)
     sCLLexSF<-sCLLex[sFiltertBH, ]

