addNormToMAGEML           package:RMAGEML           R Documentation

_A_d_d_i_n_g _a _n_o_r_m _o_b_j_e_c_t _t_o _a_n _e_x_i_s_t_i_n_g _M_A_G_E_M_L _d_o_c_u_m_e_n_t

_D_e_s_c_r_i_p_t_i_o_n:

     This function adds normalised data object obtained with limma or
     marray package to a MAGEML document.

_U_s_a_g_e:

     addNormToMAGEML(mageOM = NULL, norm = NULL, outputDirectory = ".",
     externalDataFiles = NULL, protocolID = NULL, protocol = "none", date="NA", qtID =
     NULL, qtName = NULL, qtScale = NULL, qtDataType = NULL, qtDimID =
     NULL,transformationID = NULL, DED = "none", BADIDs = NULL, derivedBioAssayIDs = NULL, derivedBioAssayDataIDs = NULL)

_A_r_g_u_m_e_n_t_s:

    norm: Normalised limma (MAList) or marray (marrayNorm) object

  mageOM: Reference to MAGE Object Model, generated by importMAGEOM()
          method.

outputDirectory: Directory where updated MAGEML document will be
          written to

externalDataFiles: List of names for external data files associated
          with a DerivedBioAssayData object.  Each filename should end
          with .txt as this is the standard output file format

protocolID: ID you want to give to the protocol, e.g. P-normalised-1

protocol: Describiption of the used protocol

    date: Date when protocol was applied

    qtID: Identifier used for the QuantitationType (the normalised
          value)

  qtName: Name for the QuantitationType

 qtScale: Scale of the QuantitationType, e.g. linear

qtDataType: DataType of the QuantitationType e.g. scalar

 qtDimID: A new QuantitationTypeDimension will be generated you'll have
          to specify it's identifier

transformationID: Identifier for the applied transformation e.g. TFM:1

     DED: DesignElementDimension corresponding to the features that are
          present in the normalised object, if only one dimension
          present in original MAGEML file then this parameter should
          not be specified

  BADIDs: List of BioAssayData identifier

derivedBioAssayIDs: List of identifiers for the DerivedBioAssay e.g.
          DBA-1

derivedBioAssayDataIDs: List of identifiers for the DerivedBioAssayData

_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','writeMAGEML'

_E_x_a_m_p_l_e_s:

     #library(RMAGEML)
     #raw<- importMAGEML(directory = "/home/steffen/data/MEXP-14")
     #norm<-maNorm(raw)
     #mageom <- importMAGEOM(directory = "/home/steffen/data/MEXP-14")
     #outputDirectory <- "/home/steffen/XMLout"
     #externalDataFile <- "deriv_test.txt"
     #protocolID <- "P-CAGE-test"
     #protocol <- "This is a test protocol! Applied maNorm."
     #qtID <- c("esat.kuleuven.ac.be:quantT-1-test", "esat.kuleuven.ac.be:quantT-2-test")
     #qtName <- c("quantitation Name 1", "quantitation Name 2")
     #qtScale <- c("linear","linear")
     #qtDataType <- c("scalar","scalar")
     #qtDimID <- "esat.kuleuven.ac.be:QTD-test"
     #BADIDs <- c("esat.kuleuven.ac.be:BAD-test1","esat.kuleuven.ac.be:BAD-test2")
     #derivedBioAssayIDs <- c("esat.kuleuven.ac.be:DBA-test1","esat.kuleuven.ac.be:DBA-test2")
     #derivedBioAssayDataIDs <- c("esat.kuleuven.ac.be:DBD-test1", "esat.kuleuven.ac.be:DBD-test2")
     #addNormToMAGEML(mageOM = mageom, norm = norm, outputDirectory = outputDirectory, externalDataFile = externalDataFile, protocolID = protocolID, protocol = protocol,  qtID = qtID, qtName = qtName, qtScale = qtScale, qtDataType = qtDataType, qtDimID = qtDimID, DED = "none", BADIDs = BADIDs, derivedBioAssayIDs = derivedBioAssayIDs, derivedBioAssayDataIDs = derivedBioAssayDataIDs)

