mmgmos                package:mmgmos                R Documentation

_M_u_l_t_i-_c_h_i_p _m_o_d_i_f_i_e_d _g_a_m_m_a _M_o_d_e_l _f_o_r _O_l_i_g_o_n_u_c_l_e_o_t_i_d_e _S_i_g_n_a_l

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

     This function converts an object of class 'AffyBatch' into an
     object of class  'exprReslt' using the Multi-chip modified gamma
     Model for Oligonucleotide Signal  (multi-mgMOS). This function
     obtains confidence of measures, standard deviation and 5,  25, 50,
     75 and 95 percentiles, as well as the estimated expression levels.

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

     mmgmos(object, savepar=FALSE, eps=1.0e-6)

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

  object: an object of 'AffyBatch'

 savepar: Logical value. If 'TRUE' the estimated parameters of the
          model are saved in file par.txt and phi.txt. 

     eps: Optimisation termination criteria.

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

     The obtained expression measures are in log base 2 scale.

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

     An object of class 'exprReslt'.

_A_u_t_h_o_r(_s):

     Xuejun Liu, Magnus Rattray, Marta Milo, Neil D. Lawrence

_R_e_f_e_r_e_n_c_e_s:

     Liu,X., Milo,M., Lawrence,N.D. and Rattray,M. (2005) A tractable
     probabilistic model for  Affymetrix probe-level analysis across
     multiple chips, technical report available upon request.

     Milo,M., Niranjan,M., Holley,M.C., Rattray,M. and Lawrence,N.D.
     (2004) A probabilistic approach for summarising  oligonucleotide
     gene expression data, technical report available upon request.

     Milo,M., Fazeli,A., Niranjan,M. and Lawrence,N.D. (2003) A
     probabilistic model for the extractioin of expression levels from
     oligonucleotide arrays, Biochemical Society Transactions, 31:
     1510-1512.

     Peter Spellucci. DONLP2 code and accompanying documentation.
     Electronically available via  http://plato.la.asu.edu/donlp2.html

_S_e_e _A_l_s_o:

     Related class 'exprReslt-class' and related method 'mgmos'

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

     ## load example data from package Affy
     data(affybatch.example)

     ## use method mmgmos to calculate the expressiong levels and related confidence 
     ## of the measures for the example data
     eset<-mmgmos(affybatch.example)

