Question: cellHTS2 writeReport error
0
gravatar for Becky Saunders
11.4 years ago by
Becky Saunders40 wrote:
Hi there, Could someone help me with the following error when I try to execute the writeReport command using cellHTS2 version 2.4.0, R version 2.7.0. out <- writeReport(cellHTSlist=list(raw=x), outdir=file.path(outHTMLDir, "raw"), force=TRUE) Error in plotScreen(ldat, zrange = range(mtW), fill = wellCols, nx = pdim(x)[["ncol"]], : 'fill' must have length >=2 since it is used to compute the color ramp that represent the values in z. I think the problem originates because I have not set a positive control in my plateConf file, as when I run the exact same input files with a positive control set it works fine. Is it possible to run the analysis without a positive control set? Also is it possible to set an argument to not include the configurationAsScreenPlot figure in the report, as you can do for plotPlateArgs and imageScreenArgs when you call writeReport? Many Thanks, Becky ===========R Console ================= > x <- readPlateList("plateList.txt", name="Automated Preliminary Analysis", path=dataPath) Automated Preliminary Analysis: found data in 8 x 12 (96 well) format. Reading 1: plate_1.txt Read 1 plates. > descripFile = file.path(dataPath, "description.txt") > confFile= file.path(dataPath, "plateConf.txt") > x <- configure(x, confFile=confFile, descripFile=descripFile) > out <- writeReport(cellHTSlist=list(raw=x), outdir=file.path(dataPath, "raw"), force=TRUE) Error in plotScreen(ldat, zrange = range(mtW), fill = wellCols, nx = pdim(x)[["ncol"]], : 'fill' must have length >=2 since it is used to compute the color ramp that represent the values in z. ===================================== -- High Throughput Screening Laboratory London Research Institute Cancer Research UK Tel No. +44 (0)207 269 3159 Fax No +44 (0) 207 269 3581 <http: www.cancerresearchuk.org=""/> -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: plateConf.txt URL: <https: stat.ethz.ch="" pipermail="" bioconductor="" attachments="" 20080716="" 49634edb="" attachment.txt=""> -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: plateList.txt URL: <https: stat.ethz.ch="" pipermail="" bioconductor="" attachments="" 20080716="" 49634edb="" attachment-0001.txt=""> -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: plate_1.txt URL: <https: stat.ethz.ch="" pipermail="" bioconductor="" attachments="" 20080716="" 49634edb="" attachment-0002.txt="">
cellhts2 • 547 views
ADD COMMENTlink modified 11.4 years ago by rclement20 • written 11.4 years ago by Becky Saunders40
Answer: cellHTS2 writeReport error
0
gravatar for rclement
11.4 years ago by
rclement20
rclement20 wrote:
Hi Becky, could you please also send the file "description.txt" ? Thanks Remy Becky Saunders wrote: > Hi there, > > Could someone help me with the following error when I try to execute the > writeReport command using cellHTS2 version 2.4.0, R version 2.7.0. > > out <- writeReport(cellHTSlist=list(raw=x), outdir=file.path(outHTMLDir, > "raw"), force=TRUE) > > Error in plotScreen(ldat, zrange = range(mtW), fill = wellCols, nx = > pdim(x)[["ncol"]], : 'fill' must have length >=2 since it is used to > compute the color ramp that represent the values in z. > > I think the problem originates because I have not set a positive control > in my plateConf file, as when I run the exact same input files with a > positive control set it works fine. Is it possible to run the analysis > without a positive control set? > > Also is it possible to set an argument to not include the > configurationAsScreenPlot figure in the report, as you can do for > plotPlateArgs and imageScreenArgs when you call writeReport? > > Many Thanks, > > Becky > > > ===========R Console ================= > > >> x <- readPlateList("plateList.txt", name="Automated Preliminary >> > Analysis", path=dataPath) > Automated Preliminary Analysis: found data in 8 x 12 (96 well) format. > > Reading 1: plate_1.txt > Read 1 plates. > > >> descripFile = file.path(dataPath, "description.txt") >> confFile= file.path(dataPath, "plateConf.txt") >> x <- configure(x, confFile=confFile, descripFile=descripFile) >> out <- writeReport(cellHTSlist=list(raw=x), outdir=file.path(dataPath, >> > "raw"), force=TRUE) > Error in plotScreen(ldat, zrange = range(mtW), fill = wellCols, nx = > pdim(x)[["ncol"]], : > 'fill' must have length >=2 since it is used to compute the color ramp > that represent the values in z. > > > ===================================== > -- > > High Throughput Screening Laboratory > London Research Institute > Cancer Research UK > > Tel No. +44 (0)207 269 3159 > > Fax No +44 (0) 207 269 3581 > > <http: www.cancerresearchuk.org=""/> > > > -------------------------------------------------------------------- ---- > > _______________________________________________ > 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
ADD COMMENTlink written 11.4 years ago by rclement20
Sorry, I didn't think you would need it. Here it is. Many thanks. -----Original Message----- From: rclement [mailto:rclement@ebi.ac.uk] Sent: 17 July 2008 09:47 To: Becky Saunders Cc: bioconductor at stat.math.ethz.ch Subject: Re: [BioC] cellHTS2 writeReport error Hi Becky, could you please also send the file "description.txt" ? Thanks Remy Becky Saunders wrote: > Hi there, > > Could someone help me with the following error when I try to execute > the writeReport command using cellHTS2 version 2.4.0, R version 2.7.0. > > out <- writeReport(cellHTSlist=list(raw=x), > outdir=file.path(outHTMLDir, "raw"), force=TRUE) > > Error in plotScreen(ldat, zrange = range(mtW), fill = wellCols, nx = > pdim(x)[["ncol"]], : 'fill' must have length >=2 since it is used to > compute the color ramp that represent the values in z. > > I think the problem originates because I have not set a positive > control in my plateConf file, as when I run the exact same input files > with a positive control set it works fine. Is it possible to run the > analysis without a positive control set? > > Also is it possible to set an argument to not include the > configurationAsScreenPlot figure in the report, as you can do for > plotPlateArgs and imageScreenArgs when you call writeReport? > > Many Thanks, > > Becky > > > ===========R Console ================= > > >> x <- readPlateList("plateList.txt", name="Automated Preliminary >> > Analysis", path=dataPath) > Automated Preliminary Analysis: found data in 8 x 12 (96 well) format. > > Reading 1: plate_1.txt > Read 1 plates. > > >> descripFile = file.path(dataPath, "description.txt") confFile= >> file.path(dataPath, "plateConf.txt") x <- configure(x, >> confFile=confFile, descripFile=descripFile) out <- >> writeReport(cellHTSlist=list(raw=x), outdir=file.path(dataPath, >> > "raw"), force=TRUE) > Error in plotScreen(ldat, zrange = range(mtW), fill = wellCols, nx = > pdim(x)[["ncol"]], : > 'fill' must have length >=2 since it is used to compute the color > ramp that represent the values in z. > > > ===================================== > -- > > High Throughput Screening Laboratory > London Research Institute > Cancer Research UK > > Tel No. +44 (0)207 269 3159 > > Fax No +44 (0) 207 269 3581 > > <http: www.cancerresearchuk.org=""/> > > > ---------------------------------------------------------------------- > -- > > _______________________________________________ > 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 -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: description.txt URL: <https: stat.ethz.ch="" pipermail="" bioconductor="" attachments="" 20080717="" 8d4f6bdd="" attachment.txt="">
ADD REPLYlink written 11.4 years ago by Becky Saunders40
Hi again Becky, "description.txt" was not really necessary indeed, but I wanted to reproduce exactly what you did :) So I got the some error message, below is what is happening : 'writeReport' calls 'configurationAsScreenPlot' : res <- makePlot( ... ... fun = function() { do.call("configurationAsScreenPlot", args=list(x=xr, verbose=FALSE, posControls=unlist(posControls), negControls=negControls)) }, ... ... and then 'configurationAsScreenPlot' calls 'plotScreen' : plotScreen(ldat, zrange=range(mtW), fill=wellCols, in 'configurationAsScreenPlot' we have above the previous command this line : wellCols <- wellCols[names(wellCols) %in% unique(wellAnnotation)] in your case, before this line, wellCols contains 3 colors sample other empty "#999999" "#000000" "#FFFFFF" and after this line, because there are only samples in your plate and no controls, wellCols contains only 1 color : sample "#999999" which is a problem for 'plotScreen', as its doc says : fill: A character vector of colors to create a color ramp for the false color data representation. At least two colors must be specified. That explains why there are no problems when you set a positive control, and it should work as well if you set a negative control instead, because after you set a control wellCols contains 2 elements and 'plotScreen' is happy with it. Now for your questions, I would answer : * you can run the analysis without a positive control set if you skip the configuration step x <- configure(x, confFile=confFile, descripFile=descripFile) and use 'writeReport' after 'readPlateList'. Is it ok for what you need ? * if you decide to configure your cellHTS object 'x', then it is not possible yet not to include the configurationAsScreenPlot figure in the report. Anyway, thanks for reporting this, it may be a good idea for a next release of cellHTS to enable the user to decide if he wants to include this figure or not. Hope it helps a little. Remy Becky Saunders wrote: > Sorry, I didn't think you would need it. > > Here it is. > > Many thanks. > > -----Original Message----- > From: rclement [mailto:rclement@ebi.ac.uk] > Sent: 17 July 2008 09:47 > To: Becky Saunders > Cc: bioconductor@stat.math.ethz.ch > Subject: Re: [BioC] cellHTS2 writeReport error > > Hi Becky, > > could you please also send the file "description.txt" ? > > Thanks > Remy > > > Becky Saunders wrote: > >> Hi there, >> >> Could someone help me with the following error when I try to execute >> the writeReport command using cellHTS2 version 2.4.0, R version 2.7.0. >> >> out <- writeReport(cellHTSlist=list(raw=x), >> outdir=file.path(outHTMLDir, "raw"), force=TRUE) >> >> Error in plotScreen(ldat, zrange = range(mtW), fill = wellCols, nx = >> pdim(x)[["ncol"]], : 'fill' must have length >=2 since it is used to >> > > >> compute the color ramp that represent the values in z. >> >> I think the problem originates because I have not set a positive >> control in my plateConf file, as when I run the exact same input files >> > > >> with a positive control set it works fine. Is it possible to run the >> analysis without a positive control set? >> >> Also is it possible to set an argument to not include the >> configurationAsScreenPlot figure in the report, as you can do for >> plotPlateArgs and imageScreenArgs when you call writeReport? >> >> Many Thanks, >> >> Becky >> >> >> ===========R Console ================= >> >> >> >>> x <- readPlateList("plateList.txt", name="Automated Preliminary >>> >>> >> Analysis", path=dataPath) >> Automated Preliminary Analysis: found data in 8 x 12 (96 well) format. >> >> Reading 1: plate_1.txt >> Read 1 plates. >> >> >> >>> descripFile = file.path(dataPath, "description.txt") confFile= >>> file.path(dataPath, "plateConf.txt") x <- configure(x, >>> confFile=confFile, descripFile=descripFile) out <- >>> writeReport(cellHTSlist=list(raw=x), outdir=file.path(dataPath, >>> >>> >> "raw"), force=TRUE) >> Error in plotScreen(ldat, zrange = range(mtW), fill = wellCols, nx = >> pdim(x)[["ncol"]], : >> 'fill' must have length >=2 since it is used to compute the color >> ramp that represent the values in z. >> >> >> ===================================== >> -- >> >> High Throughput Screening Laboratory >> London Research Institute >> Cancer Research UK >> >> Tel No. +44 (0)207 269 3159 >> >> Fax No +44 (0) 207 269 3581 >> >> <http: www.cancerresearchuk.org=""/> >> >> >> ---------------------------------------------------------------------- >> -- >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> > > [[alternative HTML version deleted]]
ADD REPLYlink written 11.4 years ago by rclement20
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