getNormalizedResponse: It combines Retention time Correction Scores (RCS) and...
In IPO: Automated Optimization of XCMS Data Processing parameters

Description Usage Arguments Details Value Note Author(s) See Also Examples

View source: R/optimizeRetCorGroupParameters.R

This function does unity based normalization on Retention time Correction Scores (RCS) as well as Grouping Scores (GS).

1	getNormalizedResponse(response)

response

A List of all responses calculated by getRGTVValues for all experiments of an Design of Experiment

Grouping Score (GS) is calculated by:
'good groups'^2/'bad groups

For all RCS and GS values unitiy based normalization is done. For every experiment within the DoE these two values are added together and returned.

A vector with RTGV values

Since RCS and GS can be within completely different ranges, normalization has to be done to prevent an excessive influence of either RCS or GS.

Gunnar Libiseller

getRGTVValues

mtbls2files <- list.files(file.path(find.package("mtbls2"), "mzData"), 
                          full.names=TRUE)

params <- list(min_peakwidth=12, max_peakwidth=30, ppm=30,
                  mzdiff=-0.001, snthresh=10, noise=10000, prefilter=3, 
                  value_of_prefilter=100,  mzCenterFun="wMean", integrate=1, 
                  fitgauss=FALSE, verbose.columns=FALSE, nSlaves=2)

xset <- calculateXcmsSet(mtbls2files[1:2], params)
xset <- retcor(xset, method="obiwarp")
xset <- group(xset)

result <- getRGTVValues(xset)
result