[BioC] error with getMeasureRepAgreement()

[Wolfgang Huber]

Dear Ning,

thank you for the code example. I think the problem lies in the line

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

which you execute *after* computing the scored and summarised xsc, hence 
in effect overwriting it. In fact, the error message seems to be quite 
descriptive of the problem (which btw it seems has nothing to do with 
your choice of corr.method = "pearson").

For next time, I suggest:
- make your example reproducible (the directory/dataset "mcherry" is 
private to your computer).
- mention the name of the package (cellHTS2) in the subject line or 
somewhere prominent.

Also note that the example datasets that come with the cellHTS2 package 
are stored in within the package, hence the
     dataPath = system.file(experimentName, package="cellHTS2"),
but you can put your own data whereever you like on the file system, 
just set "dataPath" accordingly.

	Best wishes
	Wolfgang




Ning scripsit 10/08/10 22:46:
> error with getMeasureRepAgreement()
>
>
> Hi,
> I want to use "pearson" rather than "spearman". So I made such a change:
> xsc<- getMeasureRepAgreement(xn, corr.method = "pearson")
> However an error happened:
> Error in cellHTSlistVerification (xr = raw, xn = normalized, xsc = scored, :
>    The component 'scored' of 'cellHTSlist' should be a 'cellHTS' object
> containing scored data!
> Please check its preprocessing state: configured = TRUE, normalized = TRUE,
> scored = FALSE, annotated = TRUE
> Does anyone have any ideas about it?
>
> Many thanks!
>
> Ning
>
>
> sessionInfo()
> cellHTS2
> R version 2.11.1(2010-05-31)
>
> The following is the code:
>
> experimentName<- "mcherry"
> dataPath<- system.file(experimentName, package="cellHTS2")
> x<- readPlateList("Platelist.txt",
> name=experimentName,
> path=dataPath)
> x<- configure(x,
> descripFile="Description.txt",
> confFile="Plateconf.txt",
> logFile="Screenlog.txt",
> path=dataPath)
> xn<- normalizePlates(x,
> scale="multiplicative",
> log=FALSE,
> method="NPI",
> varianceAdjust="none")
> xsc<- getMeasureRepAgreement(xn, corr.method = "pearson")
> xsc<- scoreReplicates(xn, sign="-", method="zscore")
> xsc<- summarizeReplicates(xsc, summary="median")
> xsc<- annotate(xn, geneIDFile="GeneIDs.txt",
> path=dataPath)
> 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,outdir="C:\\Documents and
> Settings\\lin6\\Desktop\\R\\mcherry",force=TRUE)
> browseURL(out)
>
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-- 


Wolfgang Huber
EMBL
http://www.embl.de/research/units/genome_biology/huber