readMageRaw              package:MAGEML              R Documentation

_C_r_e_a_t_i_o_n _o_f _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 by using the maLayout and
     maInfo available from readMageDesign and the raw data file.

_U_s_a_g_e:

     readMageRaw(fname, datadir = ".", name.Gf = "", name.Gb ="", name.Rf =
     "", name.Rb="", name.W=NULL, layout = NULL, gnames = NULL, notes=NULL, skip=0, sep="\t",quote="",...)

_A_r_g_u_m_e_n_t_s:

   fname: File name of file which contains the BioAssayData package

 datadir: Directory where the files reside

 name.Gf: Name of green foreground channel

 name.Gb: Name of green background channel

 name.Rf: Name of red foreground channel

 name.Rb: Name of red background channel

  name.W: Name of weights

   notes: object of class character, vector of explanatory text

  layout: The name of the marnotes=NULLrayLayout object that describes
          the layout of your experiment (made with readMageDesign).

  gnames: The name of the marrayInfo object that describes the genes of
          your experiment (made with readMageDesign).

     ...: Further arguments for the `scan' function

    skip: Further arguments for the `scan' function

   quote: Further arguments for the `scan' function

     sep: Further arguments for the `scan' function

_A_u_t_h_o_r(_s):

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

_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:

     'showQuantitationTypes','readMageDesign'

_E_x_a_m_p_l_e_s:

     data<-system.file("data", package="MAGEML")
     #To obtain list of available quantitation types.#
     showQuantitationTypes("Iron.xml",datadir=data)
     readMageRaw(fname="Iron.xml",datadir=data,name.Gf="ch1vol",name.Rf="ch2vol",name.Rb="ch2bgmedian",name.Gb="ch1bgmedian")
     if(interactive()){
     widget.readMageRaw()
     }

