[BioC] cellHTS2 PlateList order problem
Hahne, Florian
florian.hahne at novartis.com
Mon Jun 17 09:01:41 CEST 2013
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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