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Ning
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@ning-4161
Last seen 10.3 years ago
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)