makeMarrayRaw            package:RMAGEML            R Documentation

_C_r_e_a_t_i_o_n _o_f _a _m_a_r_r_a_y_R_a_w _o_b_j_e_c_t

_D_e_s_c_r_i_p_t_i_o_n:

     This function creates a marrayRaw object.

_U_s_a_g_e:

     makeMarrayRaw(mageOM, layout, gnames, directory = ".", DED = "none", QTD = "none", name.Rf = "none", name.Rb = "none", name.Gf = "none" ,name.Gb = "none")

_A_r_g_u_m_e_n_t_s:

  mageOM: Reference to MAGE Object Model

directory: Directory which contains the MAGEML files that need to be
          imported

  gnames: the Gnames marrayInfo object e.g. created by getGnames

  layout: the marrayLayout object e.g. created by getLayout

     QTD: the Quantitation Type Dimension

     DED: the Design Element Dimension

 name.Rf: the name of the red foreground intensity

 name.Rb: the name of the red background intensity

 name.Gf: the name of the green foreground intensity

 name.Gb: the name of the green background intensity

_A_u_t_h_o_r(_s):

     Steffen Durinck, <URL: http://www.esat.kuleuven.ac.be/~sdurinck>
       Joke Allemeersch, <URL:
     http://www.esat.kuleuven.ac.be/~jallemee>.

_R_e_f_e_r_e_n_c_e_s:

     Spellman PT, Miller M, Stewart J, Troup C, Sarkans U, Chervitz S,
     Bernhart D, Sherlock G, Ball C, Lepage M, Swiatek M, Marks WL,
     Goncalves J, Markel S, Iordan D, Shojatalab M, Pizarro A, White J,
     Hubley R, Deutsch E, Senger M, Aronow BJ, Robinson A, Bassett D,
     Stoeckert CJ Jr and Brazma A. Design and implementation of
     microarray gene expression markup language (MAGE-ML). Genome Biol.
     2002 Aug 23;3(9):RESEARCH0046.

_S_e_e _A_l_s_o:

     'importMAGEOM', 'getGnames', 'getArrayLayout'

_E_x_a_m_p_l_e_s:

     data<-system.file("MAGEMLdata", package="RMAGEML")
     #To obtain a marrayInfo object containing the database identifiers of the features present on the array.#
     mageom<-importMAGEOM(directory=data)
     gnames<-getGnames(mageom, DED = "DED:707")
     layout<-getArrayLayout(mageom)
     makeMarrayRaw(mageOM=mageom, layout = layout, gnames = gnames, directory = data, DED = "DED:707",QTD = "QTD:707", name.Rf = "QT:F635 Mean", name.Rb = "QT:B635 Median", name.Gf = "QT:F532 Mean" ,name.Gb = "QT:B532 Median")

