importMAGEML             package:RMAGEML             R Documentation

_i_m_p_o_r_t _M_A_G_E_M_L _d_o_c_u_m_e_n_t_s

_D_e_s_c_r_i_p_t_i_o_n:

     This function imports MAGEML documents and creates a marrayRaw
     object.

_U_s_a_g_e:

     importMAGEML(directory = ".", package = "marray", 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:

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

 package: name of package to which the MAGEML should be imported

     DED: the DesignElement Dimension

     QTD: the Quantitation Type 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:

     'getGnames','getArrayLayout', 'makeMarrayRaw'

_E_x_a_m_p_l_e_s:

     data<-system.file("MAGEMLdata", package="RMAGEML")
     #will return marrayRaw object.#
     importMAGEML(directory = data, package = "marray", 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")

