transform.ProbeSet         package:affypdnn         R Documentation

_A _f_u_n_c_t_i_o_n _t_o _t_r_a_n_s_f_o_r_m _a _P_r_o_b_e_S_e_t

_D_e_s_c_r_i_p_t_i_o_n:

     A function to transform the PMs and MMs in a ProbeSet.

_U_s_a_g_e:

     ## S3 method for class 'ProbeSet':
     transform(`_data`, fun = I, ...)

_A_r_g_u_m_e_n_t_s:

   _data: object of 'ProbeSet-class'.

     fun: a function. The identity function by default.

     ...: optional arguments for 'fun'.

_D_e_t_a_i_l_s:

     The function 'fun' is applied to the slots 'pm' and 'mm'. The
     function 'vsnh' in the package 'vsn' is a recommended argument for
     'fun'.

_V_a_l_u_e:

     An object of class 'ProbeSet'.

_N_o_t_e:

     This function should make to the package 'affy' for the version
     1.4.x.

_A_u_t_h_o_r(_s):

     Laurent

_E_x_a_m_p_l_e_s:

     library(affydata)

     data(Dilution)

     ppset.name <- sample(featureNames(Dilution), 1)
     ppset <- probeset(Dilution, ppset.name)[[1]]
     ppset.log <- transform(ppset, fun=log)

     par(mfrow=c(1,2))
     plot(ppset)
     plot(ppset.log)

