addNormToMAGEML {RMAGEML} | R Documentation

## Adding a norm object to an existing MAGEML document

### Description

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

### Usage

    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)

### Arguments

`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

### Author(s)

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

### References

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.

### See Also

`importMAGEOM`,`writeMAGEML`

### Examples

    #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)

[Package RMAGEML version 2.1.0 Index]