[BioC] Newbie 'rflowcyt' question; problem loading facscan256.fcs
Ulrik Stervbo
ulriks at ruc.dk
Thu May 25 08:15:35 CEST 2006
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
> >
>
--
Ulrik Stervbo
Cantianstrasse 23
10437 Berlin
Germany
Home: +49 30 441 12 81
Handy: +49 178 145 82 31
Blog: http://ulrikstervbo.blogspot.com
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