[BioC] cellHTS2 PlateList order problem

[Wolfgang Huber]

Dear Mark

firstly - many thanks for all your testing, finding this bug and reporting it with a minimal, elegant code example. This is much appreciated.
 
I reproduced the problem. AfaIcs, the bug is not in 'readPlateList' (and the object 'x' is created fine), but in the 'writeReport' function, where it affects the way the plate list table is output and ornamented with links in the HTML code. It is buried deep inside the monster that is the 'writeReport' code. I will get in touch with the maintainer and with the author of that part of the package to find the best way for fixing this.

Please keep sending such reports - while the package has no doubt lots of useful functionality, some of its code (esp. 'writeReport') has become rather involved over the years. It will be good to maintain and further develop it, since it keeps being useful for various projects. Your and others' input is very welcome.

Best wishes
	Wolfgang


On 22 May 2013, at 05:47, Mark Dane <markdane08 at gmail.com> wrote:

> Hi,
> 
> I believe there is an error in readPlateList. I can reproduce it in the KcViab data set by changing the order the files are listed.  For instance, moving the last file in Platelist.txt up to the first position like this:
> 
> Filename	Plate	Replicate
> FT57-G02.txt	57	2
> FT01-G01.txt	1	1
> .
> .
> and then executing:
> 
> library("cellHTS2")
> data(KcViab)
> experimentName <- "KcViab"
> dataPath <- system.file(experimentName, package="cellHTS2")
> x <- readPlateList("Platelist.txt",name=experimentName,path=dataPath)
> out <- writeReport(raw=x, outdir="KcViab/",force=TRUE)
> browseURL(out)
> 
> results in the data from the last file (plate 57 replica 2, channel 1) being displayed as if it is in the first file (plate 1, replica 1, channel 1)
> 
> An easy work around is to just order the files sequentially. I don't think that is the intention, though.
> 
> Otherwise, I'm making progress with large, multichannel data sets.
> 
> thank you,
> 
> Mark Dane
> Computational Biology Master Student
> Oregon Health and Science University
> 
> 
> 
> 
>> sessionInfo()
> R version 3.0.0 (2013-04-03)
> Platform: x86_64-apple-darwin10.8.0 (64-bit)
> 
> locale:
> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
> 
> attached base packages:
> [1] grid      parallel  stats     graphics  grDevices utils     datasets  methods   base     
> 
> other attached packages:
> [1] lattice_0.20-15    gdata_2.12.0.2     cellHTS2_2.25.1    locfit_1.5-9.1    
> [5] hwriter_1.3        vsn_3.29.0         splots_1.27.0      genefilter_1.43.0 
> [9] Biobase_2.21.2     BiocGenerics_0.7.2 RColorBrewer_1.0-5
> 
> loaded via a namespace (and not attached):
> [1] affy_1.39.2           affyio_1.29.0         annotate_1.39.0       AnnotationDbi_1.23.11
> [5] BiocInstaller_1.11.1  Category_2.27.1       DBI_0.2-7             graph_1.39.0         
> [9] GSEABase_1.23.0       gtools_2.7.1          IRanges_1.19.8        limma_3.17.12        
> [13] MASS_7.3-26           prada_1.37.0          preprocessCore_1.23.0 RBGL_1.37.2          
> [17] robustbase_0.9-7      rrcov_1.3-3           RSQLite_0.11.3        splines_3.0.0        
> [21] stats4_3.0.0          survival_2.37-4       tools_3.0.0           XML_3.95-0.2         
> [25] xtable_1.7-1          zlibbioc_1.7.0 
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