[BioC] cellHTS2 PlateList order problem

[Mark Dane]

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