[BioC] cellHTS2 PlateList order problem

[Hahne, Florian]

Hi Mark,
this bug should now be fixed in both the release (2.24.1) and the devel
version (2.25.6). It may take a day or two for this to make it through the
build system. You will also have to update the prada package which had to
change too.
Cheers,
Florian


On 5/22/13 5:47 AM, "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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