justMAS              package:simpleaffy              R Documentation

_G_e_n_e_r_a_t_e _E_x_p_r_e_s_s_i_o_n _c_a_l_l_s _u_s_i_n_g _a _C _i_m_p_l_e_m_e_n_t_a_t_i_o_n _o_f _t_h_e _M_A_S _5._0 _A_l_g_o_r_i_t_h_m

_D_e_s_c_r_i_p_t_i_o_n:

     Implements the MAS5.0 background correction, expression summary
     and scaling functions as described in Affy's 'Statistical
     Algorithms Description Document'

_U_s_a_g_e:

       justMAS(unnormalised,tgt=100,scale=TRUE)

_A_r_g_u_m_e_n_t_s:

unnormalised: An unnormalised AffyBatch object 

     tgt: The target intensity to scale array to, if scaling.

   scale: Scale the data to the specified target intensity.

_D_e_t_a_i_l_s:

     Uses a C code implementation of the MAS5.0 algorithm (As described
     in Affymetrix's 'Statistical Algorithms Reference Guide' - see 
     <URL: http://www.affymetrix.com>, and in Hubbell et al. (2002)
     Robust Estimators for expression analysis. Bioinformatics 18(12)
     1585-1592). Note that this function returns log2 data.

_V_a_l_u_e:

     An AffyBatch object, with, in addition, scale-factors for each
     array stored in the object's 'description@preprocessing@sfs' slot,
     and the target intensity the arrays were scaled to in 
     'description@preprocessing@tgt'

_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:

     <URL:
     http://www.affymetrix.com/support/technical/technotes/statistical_
     reference_guide.pdf>

_E_x_a_m_p_l_e_s:

      
        ## Not run: 
          eset.mas <- justMAS(eset.mas);    
        
     ## End(Not run)

