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")

