Question: cellHTS2: help with ConfFile (convertWellCoordinates) function
0
11.8 years ago by
Hi all , I have a problem when configuring my files in CellHTS2. Primarily, I get an error concerning my ConfFile which says the following- Error in convertWellCoordinates(slog$Well, pdim(object)) : 'x' must be either a character vector with alphanumeric well IDs (e.g. 'B03' or c('B', '03')) or a vector of integers with position IDs within a plate (e.g. 27). My Plateconf.txt file looks like this, which to me seems the right format. However, regardless of whether I specify each plate and well as below, or use the compressed format shown in the cellHTS2 vignette I still get the same error. Wells: 96 Plates: 18 Plate Well Content 1 A01 Neg 1 A02 Neg 1 A03 Sample 1 A04 Sample 1 A05 Sample 1 A06 Sample My only na?ve idea is that while generating the tab delinated txt file using exell that the final well descriptions are not recognised as alphanumeric by cellHTS2. I have tried generating the file in notepad but with no success. Is there some other way I should be generating the plateConf file? I have even adapted the ConfFile from the KcViab example folder and stil get the same error. I have attached a copy of my ConfFile if necessary Any help would be greatfully appreciated. Dara Dunican Cell Signalling Group, Institute of Molecular Medicine, Trinity College Dublin, Ireland cellhts2 • 436 views ADD COMMENTlink modified 11.8 years ago by Wolfgang Huber13k • written 11.8 years ago by dunicadj@tcd.ie10 Answer: cellHTS2: help with ConfFile (convertWellCoordinates) function 0 11.8 years ago by EMBL European Molecular Biology Laboratory Wolfgang Huber13k wrote: Dear Dara, the attachment didn't get through the mailing list, can you send it to me privately (ideally, send a short example script that allows me to reproduce your error, perhaps with some reduced or toy version of your data) and I'll report the solution at this place. Generating valid (for read.table) tab-delimited tables with Excel is remarkably difficult - does anyone on this list have a better suggestion of how to let users create these files (a) with a tool they like and know and (b) in a way that more robustly reads into R? Thanks and best wishes Wolfgang ------------------------------------------------------------------ Wolfgang Huber EBI/EMBL Cambridge UK http://www.ebi.ac.uk/huber dunicadj at tcd.ie scripsit: > Hi all , > > I have a problem when configuring my files in CellHTS2. Primarily, I get an > error concerning my ConfFile which says the following- > > Error in convertWellCoordinates(slog$Well, pdim(object)) : > 'x' must be either a character vector with alphanumeric well IDs (e.g. 'B03' > or c('B', '03')) > or a vector of integers with position IDs within a plate (e.g. 27). > > My Plateconf.txt file looks like this, which to me seems the right format. > However, regardless of whether I specify each plate and well as below, or use > the compressed format shown in the cellHTS2 vignette I still get the same > error. > > Wells: 96 > Plates: 18 > Plate Well Content > 1 A01 Neg > 1 A02 Neg > 1 A03 Sample > 1 A04 Sample > 1 A05 Sample > 1 A06 Sample > > My only na?ve idea is that while generating the tab delinated txt file using > exell that the final well descriptions are not recognised as alphanumeric by > cellHTS2. I have tried generating the file in notepad but with no success. > Is there some other way I should be generating the plateConf file? I have even > adapted the ConfFile from the KcViab example folder and stil get the same > error. > I have attached a copy of my ConfFile if necessary > Any help would be greatfully appreciated. > > > > Dara Dunican > Cell Signalling Group, > Institute of Molecular Medicine, > Trinity College Dublin, > Ireland > > > > > > -------------------------------------------------------------------- ---- > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
Hi Wolfgang, Wolfgang Huber schrieb: > Dear Dara, > > the attachment didn't get through the mailing list, can you send it to > me privately (ideally, send a short example script that allows me to > reproduce your error, perhaps with some reduced or toy version of your > data) and I'll report the solution at this place. > > Generating valid (for read.table) tab-delimited tables with Excel is > remarkably difficult - does anyone on this list have a better suggestion > of how to let users create these files (a) with a tool they like and > know and (b) in a way that more robustly reads into R? > I don't think that there really is a better tool than Excel, at least nothing that is widely available. This might be one of the few situations where coming up with a GUI-like thing is actually worth the effort. It seems to me that the structure of the files that need to be generated for cellHTS is fairly stable and also that the workflow should be more or less standardized at this point of a screen. Any tool that allows you to basically enter arbitrary things without any control about structure or type will eventually cause read.table to crash, there's just too many factors that can be messed up. I will try to get an overview over what is needed and think about a solution that doesn't involve too much nasty GUI programming and that is also portable over systems (bye bye to .NET...). The QT stuff seems to be very promising and Deepayan claims that things can be implemented fairly easily. The QT framework is GPL, so it could be wrapped in a standalone executable and if we wanted to we could even do things from within R. bw, Florian > Thanks and best wishes > Wolfgang > > ------------------------------------------------------------------ > Wolfgang Huber EBI/EMBL Cambridge UK http://www.ebi.ac.uk/huber > > > > dunicadj at tcd.ie scripsit: > >> Hi all , >> >> I have a problem when configuring my files in CellHTS2. Primarily, I get an >> error concerning my ConfFile which says the following- >> >> Error in convertWellCoordinates(slog$Well, pdim(object)) : >> 'x' must be either a character vector with alphanumeric well IDs (e.g. 'B03' >> or c('B', '03')) >> or a vector of integers with position IDs within a plate (e.g. 27). >> >> My Plateconf.txt file looks like this, which to me seems the right format. >> However, regardless of whether I specify each plate and well as below, or use >> the compressed format shown in the cellHTS2 vignette I still get the same >> error. >> >> Wells: 96 >> Plates: 18 >> Plate Well Content >> 1 A01 Neg >> 1 A02 Neg >> 1 A03 Sample >> 1 A04 Sample >> 1 A05 Sample >> 1 A06 Sample >> >> My only na?ve idea is that while generating the tab delinated txt file using >> exell that the final well descriptions are not recognised as alphanumeric by >> cellHTS2. I have tried generating the file in notepad but with no success. >> Is there some other way I should be generating the plateConf file? I have even >> adapted the ConfFile from the KcViab example folder and stil get the same >> error. >> I have attached a copy of my ConfFile if necessary >> Any help would be greatfully appreciated. >> >> >> >> Dara Dunican >> Cell Signalling Group, >> Institute of Molecular Medicine, >> Trinity College Dublin, >> Ireland >> >> >> >> >> >> ------------------------------------------------------------------- ----- >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >> > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > -- Florian Hahne, PhD Computational Biology Program Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M2-B876 PO Box 19024 Seattle, Washington 98109-1024 206-667-3148 fhahne at fhcrc.org ADD REPLYlink written 11.8 years ago by Florian Hahne540 Dear Dara, thank you for sending the offending data files and the script you used. The solution is very simple: your file "Screenlog.txt" was empty (i.e. it only contained the header and no data rows), and the 'configure' function stumbled over that. A work-around for you is to simply omit the 'logFile' argument from your call to 'configure' (as it is empty anyway). When starting R in the directory where the files are, the following lines worked for me: library("cellHTS2") x = readPlateList ('Platelist.txt', name='testcellHTSfiles') x = configure(x, descripFile='Description.txt', confFile='plateConf.txt') Also, we will fix the package so that it deals more gracefully with this 'trivial' special case of zero-row Screenlog files. Btw, in the code you had sent me, you had used dataPath=system.file(experimentName, package='cellHTS2'). You've probably seen this idiom in the vignette, where we use it to say where the "KcViab" example data are. While it is not wrong, it is unusual (and perhaps unnecessary) to copy your own, actual data into the directory where the R package is installed. Just put the data somewhere that makes sense to you, and set 'dataPath' to that path. > sessionInfo() R version 2.7.0 Under development (unstable) (2008-02-27 r44632) x86_64-unknown-linux-gnu locale: LC_CTYPE=it_IT.UTF-8;LC_NUMERIC=C;LC_TIME=it_IT.UTF-8;LC_COLLATE=it_IT .UTF-8;LC_MONETARY=it_IT.UTF-8;LC_MESSAGES=it_IT.UTF-8;LC_PAPER=it_IT. UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=it_IT.UTF-8 ;LC_IDENTIFICATION=C attached base packages: [1] splines grid tools stats graphics grDevices utils [8] datasets methods base other attached packages: [1] cellHTS2_2.3.19 vsn_3.4.8 limma_2.13.4 [4] affy_1.17.5 preprocessCore_1.1.5 affyio_1.7.13 [7] splots_1.5.1 genefilter_1.17.11 survival_2.34 [10] prada_1.15.0 rrcov_0.4-05 robustbase_0.2-8 [13] RColorBrewer_1.0-2 Biobase_1.17.14 fortunes_1.3-4 loaded via a namespace (and not attached): [1] annotate_1.17.11 AnnotationDbi_1.1.22 DBI_0.2-4 [4] geneplotter_1.17.7 KernSmooth_2.22-22 lattice_0.17-6 [7] MASS_7.2-41 RSQLite_0.6-7 stats4_2.7.0 Best wishes Wolfgang ------------------------------------------------------------------ Wolfgang Huber EBI/EMBL Cambridge UK http://www.ebi.ac.uk/huber Wolfgang Huber scripsit: > Dear Dara, > > the attachment didn't get through the mailing list, can you send it to > me privately (ideally, send a short example script that allows me to > reproduce your error, perhaps with some reduced or toy version of your > data) and I'll report the solution at this place. > > Generating valid (for read.table) tab-delimited tables with Excel is > remarkably difficult - does anyone on this list have a better suggestion > of how to let users create these files (a) with a tool they like and > know and (b) in a way that more robustly reads into R? > > Thanks and best wishes > Wolfgang > > ------------------------------------------------------------------ > Wolfgang Huber EBI/EMBL Cambridge UK http://www.ebi.ac.uk/huber > > > > dunicadj at tcd.ie scripsit: >> Hi all , >> >> I have a problem when configuring my files in CellHTS2. Primarily, I get an >> error concerning my ConfFile which says the following- >> >> Error in convertWellCoordinates(slog$Well, pdim(object)) : >> 'x' must be either a character vector with alphanumeric well IDs (e.g. 'B03' >> or c('B', '03')) >> or a vector of integers with position IDs within a plate (e.g. 27). >> >> My Plateconf.txt file looks like this, which to me seems the right format. >> However, regardless of whether I specify each plate and well as below, or use >> the compressed format shown in the cellHTS2 vignette I still get the same >> error. >> >> Wells: 96 >> Plates: 18 >> Plate Well Content >> 1 A01 Neg >> 1 A02 Neg >> 1 A03 Sample >> 1 A04 Sample >> 1 A05 Sample >> 1 A06 Sample >> >> My only na?ve idea is that while generating the tab delinated txt file using >> exell that the final well descriptions are not recognised as alphanumeric by >> cellHTS2. I have tried generating the file in notepad but with no success. >> Is there some other way I should be generating the plateConf file? I have even >> adapted the ConfFile from the KcViab example folder and stil get the same >> error. >> I have attached a copy of my ConfFile if necessary >> Any help would be greatfully appreciated. >> >> >> >> Dara Dunican >> Cell Signalling Group, >> Institute of Molecular Medicine, >> Trinity College Dublin, >> Ireland >>