Hi Ulrik, I was not able to reproduce your error. However I have modified the read.FCS function. Could you test the new package ? You can find the new source at: http://bioconductor.org/packages/1.9/bioc/html/rflowcyt.html Have you tried with your own dataset? Nolwenn Ulrik Stervbo wrote: >Hi Nolwenn, > >Yes, it is the read.FCS that gievs errors. > >Here's what I've done after starting R: > > >>library(rflowcyt) >>library(Biobase) >>fcs.loc <- system.file("fcs", package = "rfcdmin") >>file.location <- paste(fcs.loc, "facscan256.fcs", sep = "/") >>FC.FCSRobj <- read.FCS(file.location, UseS3 = TRUE, MY.DEBUG = TRUE,fcs.type = NULL) >> >> >Start/Stop:$version >[1] "FCS2.0" > >$TextStart >[1] 256 > >$TextEnd >[1] 1595 > >$TextLength >[1] 1340 > >$DataStart >[1] 1792 > >$DataEnd >[1] 51791 > >$DataLength >[1] 50000 > >$AnalysisStart >[1] 0 > >$AnalysisEnd >[1] 0 > >Error in if (my.metadata.Text.verbose[last] != my.metadata.delimiter) { : > missing value where TRUE/FALSE needed > >Reading in series also fails (with the same error (of course)): > > >>pathFiles <- system.file("bccrc", package = "rfcdmin") >>drugFiles <- dir(pathFiles) >>drugData <- read.series.FCS(drugFiles, path = pathFiles, MY.DEBUG = TRUE) >> >> >[1] "A06" >Start/Stop:$version >[1] "FCS2.0" > >$TextStart >[1] 256 > >$TextEnd >[1] 2270 > >$TextLength >[1] 2015 > >$DataStart >[1] 2304 > >$DataEnd >[1] 30863 > >$DataLength >[1] 28560 > >$AnalysisStart >[1] 0 > >$AnalysisEnd >[1] 0 > >Error in if (my.metadata.Text.verbose[last] != my.metadata.delimiter) { : > missing value where TRUE/FALSE needed >[1] "B06" >Start/Stop:$version >[1] "FCS2.0" > >$TextStart >[1] 256 > >$TextEnd >[1] 2271 > >$TextLength >[1] 2016 > >$DataStart >[1] 2304 > >$DataEnd >[1] 34223 > >$DataLength >[1] 31920 > >$AnalysisStart >[1] 0 > >$AnalysisEnd >[1] 0 > >Error in if (my.metadata.Text.verbose[last] != my.metadata.delimiter) { : > missing value where TRUE/FALSE needed >[1] "C06" >Start/Stop:$version >[1] "FCS2.0" > >$TextStart >[1] 256 > >$TextEnd >[1] 2271 > >$TextLength >[1] 2016 > >$DataStart >[1] 2304 > >$DataEnd >[1] 27023 > >$DataLength >[1] 24720 > >$AnalysisStart >[1] 0 > >$AnalysisEnd >[1] 0 > >Error in if (my.metadata.Text.verbose[last] != my.metadata.delimiter) { : > missing value where TRUE/FALSE needed >[1] "D06" >Start/Stop:$version >[1] "FCS2.0" > >$TextStart >[1] 256 > >$TextEnd >[1] 2271 > >$TextLength >[1] 2016 > >$DataStart >[1] 2304 > >$DataEnd >[1] 42623 > >$DataLength >[1] 40320 > >$AnalysisStart >[1] 0 > >$AnalysisEnd >[1] 0 > >Error in if (my.metadata.Text.verbose[last] != my.metadata.delimiter) { : > missing value where TRUE/FALSE needed >[1] "E06" >Start/Stop:$version >[1] "FCS2.0" > >$TextStart >[1] 256 > >$TextEnd >[1] 2271 > >$TextLength >[1] 2016 > >$DataStart >[1] 2304 > >$DataEnd >[1] 29423 > >$DataLength >[1] 27120 > >$AnalysisStart >[1] 0 > >$AnalysisEnd >[1] 0 > >Error in if (my.metadata.Text.verbose[last] != my.metadata.delimiter) { : > missing value where TRUE/FALSE needed >[1] "F06" >Start/Stop:$version >[1] "FCS2.0" > >$TextStart >[1] 256 > >$TextEnd >[1] 2271 > >$TextLength >[1] 2016 > >$DataStart >[1] 2304 > >$DataEnd >[1] 22703 > >$DataLength >[1] 20400 > >$AnalysisStart >[1] 0 > >$AnalysisEnd >[1] 0 > >Error in if (my.metadata.Text.verbose[last] != my.metadata.delimiter) { : > missing value where TRUE/FALSE needed >[1] "G06" >Start/Stop:$version >[1] "FCS2.0" > >$TextStart >[1] 256 > >$TextEnd >[1] 2271 > >$TextLength >[1] 2016 > >$DataStart >[1] 2304 > >$DataEnd >[1] 81263 > >$DataLength >[1] 78960 > >$AnalysisStart >[1] 0 > >$AnalysisEnd >[1] 0 > >Error in if (my.metadata.Text.verbose[last] != my.metadata.delimiter) { : > missing value where TRUE/FALSE needed >[1] "H06" >Start/Stop:$version >[1] "FCS2.0" > >$TextStart >[1] 256 > >$TextEnd >[1] 2271 > >$TextLength >[1] 2016 > >$DataStart >[1] 2304 > >$DataEnd >[1] 70943 > >$DataLength >[1] 68640 > >$AnalysisStart >[1] 0 > >$AnalysisEnd >[1] 0 > >Error in if (my.metadata.Text.verbose[last] != my.metadata.delimiter) { : > missing value where TRUE/FALSE needed >0 fcs files read >Warning message: >Unable to read the following files: >A06 >B06 >C06 >D06 >E06 >F06 >G06 >H06 in: read.series.FCS(drugFiles, path = pathFiles, MY.DEBUG = TRUE) > >Hope this helps :-D > >Btw, I'm running Suse 9.3 with KDE 3.4.2 > >On 5/25/06, Nolwenn LeMeur <nlemeur at="" fhcrc.org=""> wrote: > > >>Hi Ulrik, >>I am not sure what is the error. I've tried and it works fine for me. >>Which function give you that error? read.FCS? >>Have you tried to set the MY.DEBUG parameter to TRUE? >> >>Nolwenn >> >>************************************** >>Nolwenn Le Meur, PhD >>Fred Hutchinson Cancer Research Center >>Computational Biology >>1100 Fairview Ave. N., M2-B876 >>P.O. Box 19024 >>Seattle, WA 98109-1024 >> >>On Wed, 24 May 2006, Ulrik Stervbo wrote: >> >> >> >>>Hi all, >>> >>>I am all new to R and rflowcyt; I've googled and searched looked >>>through recent mailinglist archives, but to no avail... >>> >>>I am trying to load the facscan256.fcs, as described on page 5 (yes 5) >>>of 'Using RFlowCyt' from 3 April, 2006. I am stuck with this error: >>> Error in if (my.metadata.Text.verbose[last] != my.metadata.delimiter) { : >>> missing value where TRUE/FALSE needed >>> >>>I have no idea what I am doing wrong - I installed the packages with >>>getBioC(c("rflowcyt")) (as root). It looked like the packages which >>>rflowcyt depends on were also installed. >>> >>> >>> >>>>sessionInfo() >>>> >>>> >>>Version 2.3.0 (2006-04-24) >>>i686-pc-linux-gnu >>> >>>attached base packages: >>> [1] "tools" "grid" "splines" "methods" "stats" "graphics" >>> [7] "grDevices" "utils" "datasets" "base" >>> >>>other attached packages: >>> Biobase rflowcyt locfit akima fields rfcdmin hexbin >>> "1.10.0" "1.4.0" "1.5-3" "0.5-1" "2.3" "1.4.0" "1.6.0" >>>colorspace lattice splancs sp MASS KernSmooth xtable >>> "0.9" "0.13-8" "2.01-17" "0.8-14" "7.2-27" "2.22-17" "1.3-2" >>> survival >>> "2.24" >>> >>>Btw. Biobase was not loaded with > library(rflowcyt) (or require(rflowcyt)). >>> >>>The problem is probably very FAQ, I just can't find the answer. >>> >>>Thanks in advance for any help >>>Ulrik >>> >>>_______________________________________________ >>>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 >>> >>> >>> > > > >