Question: cellHTS2 PlateList order problem
0
gravatar for florian.hahne@novartis.com
6.4 years ago by
Switzerland
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 >_______________________________________________ >Bioconductor mailing list >Bioconductor at r-project.org >https://stat.ethz.ch/mailman/listinfo/bioconductor >Search the archives: >http://news.gmane.org/gmane.science.biology.informatics.conductor
multichannel prada • 428 views
ADD COMMENTlink written 6.4 years ago by florian.hahne@novartis.com1.6k
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