justmmgMOS              package:mmgmos              R Documentation

_C_o_m_p_u_t_e _m_m_g_m_o_s _D_i_r_e_c_t_l_y _f_r_o_m _C_E_L _F_i_l_e_s

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

     This function converts CEL files into an 'exprReslt' using mmgmos.

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

     justmmgMOS(..., filenames=character(0),
               widget=getOption("BioC")$affy$use.widgets,
               compress=getOption("BioC")$affy$compress.cel,
               celfile.path=getwd(),
               sampleNames=NULL,
               phenoData=NULL,
               description=NULL,
               notes="",
               background=TRUE, savepar=FALSE, eps=1.0e-6)

     just.mmgmos(..., filenames=character(0),
                phenoData=new("phenoData"),
                description=NULL,
                notes="",
                compress=getOption("BioC")$affy$compress.cel,
                background=TRUE, savepar=FALSE, eps=1.0e-6)

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

     ...: file names separated by comma.

filenames: file names in a character vector.

  widget: a logical specifying if widgets should be used.

compress: are the CEL files compressed ?

celfile.path: a character denoting the path 'ReadAffy' should look for
          cel files

sampleNames: a character vector of sample names to be used in the
          'AffyBatch'

phenoData: a 'phenoData' object

description: a 'MIAME' object

   notes: notes 

background: Logical value. If 'TRUE', perform background correction
          before applying mmgmos.

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

     eps: Optimisation termination criteria.

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

     This method should require much less RAM than the conventional
     method of first creating an 'AffyBatch' and then running 'mmgmos'.

     Note that this expression measure is given to you in log base 2
     scale. This differs from most of the other expression measure
     methods.

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

     An 'exprReslt'.

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

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

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

