[BioC] the issue with analysis of multi-channel screen

Wolfgang Huber whuber at embl.de
Tue Oct 26 22:30:47 CEST 2010


it seems that the function "scoreReplicates" does not mark the fact that 
scoring has been done in the "state" of the object, but does so in the 
"processingInfo" slot. (Type "scoreReplicates" without parentheses to 
see its simple code.)

Florian Hahne might be able to give a deeper answer, but it seems he's 
currently entertaining two partially redundant history keeping 
mechanisms in the cellHTS class. I think they are for information only 
and do not influence the computed results.

Otherwise, your code looks great, I hope you find the package useful and 
get good results out of it. Let us know if you have questions.

	Best wishes

Il Oct/22/10 11:12 PM, Ning ha scritto:
> Hi Wolfgang,
> I have 3 channels applied in screen. Two of them are used as the reporter to
> monitor the early stage of signaling pathway, the other one is for the late
> stage. The following is the script
> library("cellHTS2")
> experimentName<- "DataIntegration"
> 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)
> negCtr<- vector("character", length=dim(Data(x))[3])
> negCtr[1]<- "(?i)^ntc2-lps$"
> negCtr[2]<- "(?i)^ntc2-lps$"
> negCtr[3]<- "(?i)^ntc2-lps$"
> posCtrs<- vector("character", length=dim(Data(x))[3])
> posCtrs[1]<- list(act="(?i)^ntc2+lps$", inh="(?i)^myd88$|^tlr4$|^irak1+4$")
> posCtrs[2]<- list(act="(?i)^ntc2+lps$", inh="(?i)^myd88$|^tlr4$|^irak1+4$")
> posCtrs[3]<- list(act="(?i)^ntc2+lps$", inh="(?i)^myd88$|^tlr4$|^irak1+4$")
> xn<- normalizePlates(x,
>                        scale="multiplicative",
>                        log=FALSE,
>                        method="median",
>                        varianceAdjust="none")
> xsc<- scoreReplicates(xn, sign="+", method="zscore")
> xsc<- summarizeReplicates(xsc, summary="median")
> However, when I checked the state by calling state(xsc), the result showed XSC
> has not been scored. When I checked the xsc data by using Data(xsc), it showed
> the z score has been calculated. Do you have any idea about it?
> Many thanks
> Ning
> sessionInfo()
> cellHTS2
> R version 2.11.1(2010-05-31)
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