detection.p.val          package:simpleaffy          R Documentation

_C_a_l_c_u_l_a_t_e _D_e_t_e_c_t_i_o_n _p-_v_a_l_u_e_s

_D_e_s_c_r_i_p_t_i_o_n:

     Calculate MAS5 detection pvalues and Present Marginal Absent
     calls. This is an implementation based on the algorithm described
     in  Liu, Mei et al. (2002) 'Analysis of high density expression
     microarrays with signed-rank call algorithms', Bioinformatics
     18(12) pp1593-1599.

_U_s_a_g_e:

     detection.p.val(x, tau = NULL,calls=TRUE,alpha1=NULL,alpha2=NULL,ignore.saturated=TRUE)

_A_r_g_u_m_e_n_t_s:

       x: An unnormalised AffyBatch object 

     tau: Errrmmm... tau 

  alpha1: Present-Marginal threshold 

  alpha2: Marginal-Absent threshold 

   calls: if true, generate PMA calls 

ignore.saturated: if true do the saturation correction described in the
          paper, with a saturation level of 46000 

_V_a_l_u_e:

     A list: 

    pval: A matrix of detection p values

    call: A matrix of PMA calls

_N_o_t_e:

     alpha1 and alpha2 are parameters that change according to the chip
     type you are using. If they are not specified, the function uses
     the current QC environment to find them, and attempts to set one
     up if it is not there. This is done with an internal call to the
     function 'setQCEnvironment'. If it is unable to find the
     appropriate config files, this will cause an error. See
     'setQCEnvironment' for more details.

_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/

_S_e_e _A_l_s_o:

     'setQCEnvironment'

_E_x_a_m_p_l_e_s:

        ## Not run: 
          dpv <- detection.p.val(eset);
        
     ## End(Not run)