[BioC] [cellHTS2] error message with DualChannelScreen on example dataset

[Wolfgang Huber]

Hi Vipin

I'm assuming you got the idea for the below code from the material distributed at last week's EMBO course? Since 'summarizeReplicates' so far had not been implemented in cellHTS2 for data with more than one channel (i.e. colour). This new feature is planned for future releases of the package.

Till then, you could have a look at the lab material that was prepared by Joseph Barry: 
  http://www-huber.embl.de/users/barry/EMBO-lab-P12/

In particular, see the function summarizeReplicatesMultiChannel which is defined in the file EMBO-lab.Rnw.

Best wishes
	Wolfgang


Il giorno Oct 26, 2012, alle ore 5:50 PM, Vipin T Sreedharan <vipin at cbio.mskcc.org> ha scritto:

> Hi all!, 
> 
> We are trying to run cellHTS2 sample dataset for dual channel screen and it ended up with following error message: 
> 
> Error in summarizeReplicates(xsc, summary = "mean") : 
>  Currently this function is implemented only for single-color data.
> 
> From the FAQ it seems like this is pointing to the step 2 but this is not clear for us. 
> 
> http://rnai-screening-wiki.dkfz.de/signaling/wiki/display/rnaiwiki/web+cellHTS2+Manual
> Currently this function is implemented only for single-color data. 
> Channel 2 was labeld to one of your files in step 
> 
> The pseudo code we were trying  as follows: 
> 
>>> library("cellHTS2")
>>> expName <- "DualChannelScreen"
>>> datadir <- system.file("DualChannelScreen", package="cellHTS2")
>>> x <- readPlateList("Platelist.txt", name=expName, path=datadir)
>>> x <- configure(x, "Description.txt", "Plateconf.txt", "Screenlog.txt", path=datadir)
>>> xn = normalizePlates(x, scale="multiplicative", log=FALSE, method="median", varianceAdjust="none")
>>> xsc = scoreReplicates(xn, sign="-", method="zscore")
>>> xsc = summarizeReplicates(xsc, summary="mean")
>>> xsc = annotate(xsc, geneIDFile="GeneIDs.txt", path=datadir)
> 
> Hope someone can give more insight on this error message. 
> 
> Many thanks in advance, 
> Vipin
> 
> 
> 	[[alternative HTML version deleted]]
> 
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