NormCombined: Normalisation methods based on a combination of methods

In NormalizeMets: Analysis of Metabolomics Data

Description

Normalise a metabolomic data matrix using a combination of methods

Usage

NormCombined(featuredata, methods = c("rlsc", "median"),
  savefinaloutput = FALSE, finaloutputname = NULL, ...)

Arguments

featuredata	featuredata A data frame in the featuredata format. This is a dataframe with metabolites in columns and samples in rows. Unique sample names should be provided as row names.
methods	A character vector indicating which two methods should be used in order.
savefinaloutput	A logical indicating whether the final normalised data matrix should be saved as a .csv file.
finaloutputname	The name of the final output file if the output has to be saved.
...	Inputs for the NormScaling, NormQcmets, and NormQcsamples as appropriate.

Value

The result is an object of class alldata.

Author(s)

Alysha M De Livera, Gavriel Olshansky

References

De Livera, Alysha M De, M. Aho-Sysi, Laurent Jacob, J. Gagnon-Bartch, Sandra Castillo, J.A. Simpson, and Terence P. Speed. 2015. Statistical Methods for Handling Unwanted Variation in Metabolomics Data. Analytical Chemistry 87 (7). American Chemical Society: 3606-3615.

De Livera, A. M., Dias, D. A., De Souza, D., Rupasinghe, T., Pyke, J., Tull, D., Roessner, U., McConville, M., Speed, T. P. (2012a) Normalising and integrating metabolomics data. Analytical Chemistry 84(24): 1076-10776.

De Livera, A.M., Olshansky, M., Speed, T. P. (2013) Statistical analysis of metabolomics data. Methods in Molecular Biology In press.

Gagnon-Bartsch, Johann A., Speed, T. P. (2012) Using control genes to correct for unwanted variation in microarray data. Biostatistics 13(3): 539-552.

Redestig, H., Fukushima, A., Stenlund, H., Moritz, T., Arita, M., Saito, K., Kusano, M. (2009) Compensation for systematic cross-contribution improves normalization of mass spectrometry based metabolomics data. Analytical Chemistry 81(19): 7974-7980.

Sysi-Aho, M., Katajamaa, M., Yetukuri, L., Oresic, M. (2007) Normalization method for metabolomics data using optimal selection of multiple internal standards. BMC Bioinformatics 8(1): 93.

Dunn,W.B., Broadhurst,D., Begley,P., Zelena,E., Francis-McIntyre,S., Anderson,N., Brown,M., Knowles,J.D., Halsall,A., Haselden,J.N. et al. (2011) Procedures for large-scale metabolic profiling of serum and plasma using gas chromatography and liquid chromatography coupled to mass spectrometry. Nat. Protoc., 6, 1060-1083

Examples

 ##Reading the data
 data(Didata)
 NormCombined(featuredata=Didata$featuredata[order(Didata$sampledata$order),],
            sampledata=Didata$sampledata[order(Didata$sampledata$order),],
            methods=c("rlsc", "median"),
            savefinaloutput=FALSE, 
            finaloutputname=NULL)


    

NormalizeMets documentation built on May 1, 2019, 10:26 p.m.