call.exprs            package:simpleaffy            R Documentation

_G_e_n_e_r_a_t_e _E_x_p_r_e_s_s_i_o_n _S_u_m_m_a_r_i_e_s _f_o_r _A_f_f_y_m_e_t_r_i_x _D_a_t_a

_D_e_s_c_r_i_p_t_i_o_n:

     Generates expression summaries and normalizes Affymetrix data
     using either MAS5.0, GCRMA or RMA algorithms.

_U_s_a_g_e:

     call.exprs(x, algorithm = "rma", do.log = TRUE, sc = 100, method = NA)

_A_r_g_u_m_e_n_t_s:

       x: an 'AffyBatch' object 

algorithm: one of '"rma","rma-R","gcrma", "mas5", "mas5-R". "rma" and
          "mas5" make use of a native C-library and are faster than
          "rma-R" and "mas5-R". 

  do.log: return logged data if true 

      sc: if the mas5 algorithm is being used, sets the target
          intensity to which the chips should be scaled. 

  method: The algorithm used to normalise the data. Has no effect for
          "rma",  defaults to quantile normalisation for "rma" and no
          normalisation for "mas5" 

_D_e_t_a_i_l_s:

_V_a_l_u_e:

     An AffyBatch object containing expression summaries.

_A_u_t_h_o_r(_s):

     Crispin J Miller

_R_e_f_e_r_e_n_c_e_s:

     <URL: http://bioinformatics.picr.man.ac.uk/>

_S_e_e _A_l_s_o:

     'read.affy', 'expresso', 'justRMA', 'justMAS'

_E_x_a_m_p_l_e_s:

      
       ## Not run: 
         eset.rma  <- call.exprs(eset,"rma"); 
         eset.mas5 <- call.exprs(eset,"mas5"); 
       
     ## End(Not run)