pmcorrect                package:affy                R Documentation

_P_M _C_o_r_r_e_c_t_i_o_n

_D_e_s_c_r_i_p_t_i_o_n:

     Corrects the PM intensities in a 'ProbeSet' for nonspecific
     binding.

_U_s_a_g_e:

     pmcorrect.pmonly(object)

     pmcorrect.subtractmm(object)

     pmcorrect.mas(object, contrast.tau=0.03, scale.tau=10, delta=2^(-20))

_A_r_g_u_m_e_n_t_s:

  object: An object of class 'ProbeSet'.

contrast.tau: a number denoting the contrast tau parameter in the MAS
          5.0  pm correction algorithm.

scale.tau: a number denoting the scale tau parameter in the MAS 5.0  pm
          correction algorithm.

   delta: a number denoting the detla parameter in the MAS 5.0  pm
          correction algorithm.

_D_e_t_a_i_l_s:

     These are the pm correction methods perfromed by Affymetrix MAS
     4.0 (subtractmm) and MAS 5.0 (mas). See the Affymetrix Manual for
     details. pmonly does what you think: does not change the PM
     values.

_V_a_l_u_e:

     A 'ProbeSet' for which the 'pm' slot contains the  corrected  PM
     values.

_R_e_f_e_r_e_n_c_e_s:

     Affymetrix MAS 4.0 and 5.0 manual

_E_x_a_m_p_l_e_s:

     data(affybatch.example)
     gn <- geneNames(affybatch.example)
     pps <- probeset(affybatch.example, gn[1])[[1]]

     pps.pmonly <- pmcorrect.pmonly(pps)
     pps.subtractmm <- pmcorrect.subtractmm(pps)
     pps.mas5 <- pmcorrect.mas(pps)
     par(mfrow=c(2,2))
     #plot(pm(pps.pmonly), pm(pps.subtractmm))
     #plot(pm(pps.pmonly),pm(pps.mas5))
     #plot(pm(pps.subtractmm),pm(pps.mas5))