[BioC] The issue with Report Pearson instead of Spearman

[Ning]

Hi Wolfgang,

Thank you for your reply. Actually my question is how I can let the results of
Pearson correlation showed in the report when I use the function of writeReport.
As every time I use this function, only the results of Spearman rank correlation
were showed in the report, even I have called

repAgree <- getMeasureRepAgreement(xn, corr.method = "pearson") 

I checked the instruction of writeReport function, but cannot find the way to
put the “repAgree” in it.

My code of writeReport is

setSettings(list(plateList=list(reproducibility=list(include=TRUE, map=TRUE),
intensities=list(include=TRUE, range=c(-0.5,1), map=TRUE)),
screenSummary=list(scores=list(range=c(-4, 8), map=TRUE))))
out <- writeReport(raw=x, normalized=xn, scored=xsc,map=TRUE, force=TRUE)

Do you have any idea about where I put the “repAgree” in?
Many thanks!

Ning

The following is my script

# read platelist     
x <- readPlateList("Platelist.txt",
                    name=experimentName,
                    path=dataPath)
#Configure X
x <- configure(x,
               descripFile="Description.txt",
               confFile="Plateconf.txt",
               logFile="Screenlog.txt",
               path=dataPath)
#Normalize X
 xn <- normalizePlates(x,
       scale="multiplicative",
       log=FALSE,
       method="NPI",
       varianceAdjust="none")
 
#Calculate the Pearson correlation with normalized “xn”
repAgree <- getMeasureRepAgreement(xn, corr.method = "pearson") 

#Scored “xn”
xsc <- scoreReplicates(xn, sign="-", method="zscore") 

# summarize
xsc <- summarizeReplicates(xsc, summary="median")

# annotate
xsc <- annotate(xn, geneIDFile="GeneIDs.txt",  path=dataPath)

# write report
setSettings(list(plateList=list(reproducibility=list(include=TRUE, map=TRUE),
            intensities=list(include=TRUE, range=c(-0.5,1), map=TRUE)),
            screenSummary=list(scores=list(range=c(-4, 8), map=TRUE))))
out <- writeReport(raw=x, normalized=xn, scored=xsc,map=TRUE, force=TRUE)