[BioC] Newbie 'rflowcyt' question; problem loading facscan256.fcs
Nolwenn LeMeur
nlemeur at fhcrc.org
Mon May 29 20:10:29 CEST 2006
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
>>>
>>>
>>>
>
>
>
>
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