[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
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Blog: http://ulrikstervbo.blogspot.com



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