[R] Reading FCS files with flowCore package

Mon Nov 24 21:41:25 CET 2014

> or to change the default to mustWork=TRUE, since there are not
> many use cases for querying a non-existent system file?

There are a fair number of packages depending on the current semantics.
E.g.
  ./proxy/R/dissimilarities.R:    if (system.file(package="cba") == "")
  ./openNLP/R/pos.R:                      if(system.file(package = package)
== "") {
  ./relations/R/plot.R:    if(system.file(package = "Rgraphviz") == "")
  ./e1071/R/bclust.R:        if (system.file(package = "cluster") == "")
  ./repmis/R/utils.R:     idx = mapply(system.file, package = x) == ''
In most of those, the next statement is stop("package <name> is required")
but
in the last there is only a warning.

> (one irony I've stumbled across in my own code is to misspell 'mustWork',
> e.g., system.file("foo", mustwork=TRUE), which happily returns "").

I've run into the same issue.  Functions with ... in the argument list
often let
things go by that should not.

Bill Dunlap
TIBCO Software
wdunlap tibco.com

On Mon, Nov 24, 2014 at 12:23 PM, Martin Morgan <mtmorgan at fredhutch.org>
wrote:

> On 11/24/2014 11:38 AM, William Dunlap wrote:
>
>> If help files used the mustWork=TRUE argument to system.file() this sort
>> of problem
>> would become more apparent to the user.  It would give a clear error
>> message from
>>
>
> or to change the default to mustWork=TRUE, since there are not many use
> cases for querying a non-existent system file?
>
> (one irony I've stumbled across in my own code is to misspell 'mustWork',
> e.g., system.file("foo", mustwork=TRUE), which happily returns "").
>
> Martin
>
>  system.file() instead of a mysterious error about file "" not being valid
>> or,
>> worse, a hang
>> from an input command waiting for the user to type something into
>> standard input
>> (because
>> scan() and others treat file="" the same as scan=stdin()).
>>
>> Bill Dunlap
>> TIBCO Software
>> wdunlap tibco.com <http://tibco.com>
>>
>> On Mon, Nov 24, 2014 at 10:36 AM, Martin Morgan <mtmorgan at fredhutch.org
>> <mailto:mtmorgan at fredhutch.org>> wrote:
>>
>>     On 11/24/2014 06:18 AM, Luigi wrote:
>>
>>         Dear all,
>>         I would like to use the R's Bioconductor package flowCore to do
>> flow
>>         cytometry
>>
>>
>>     Please address questions about Bioconductor packages to the
>> Bioconductor
>>     support site
>>
>>     https://support.bioconductor.__org <https://support.bioconductor.org>
>>
>>     and...
>>
>>         analysis.
>>         I generated a FCS file using the file>export function of the
>> FACSDiva
>>         Software
>>         Version 8 from a BD LSRII machine. I then used the functions:
>>         file.name <http://file.name> <-system.file("extdata", "cd
>> cells_FMO
>>         8_003.fcs",
>>         package="flowCore")
>>
>>
>>     system.file() is used to access files installed in R packages, but
>> probably
>>     you want to access your own file. Try
>>
>>     file.name <http://file.name> = file.choose()
>>
>>     and selecting the file that you want to iniptu. Verify that the path
>> is
>>     correct by displaying the result
>>
>>     file.name <http://file.name>
>>
>>     Martin
>>
>>               x <-read.FCS(file.name <http://file.name>, transformation
>> = FALSE)
>>         as shown in the flowCore: data structure package... vignette (20
>> May
>>         2014) as
>>         available from the internet. However the result is an error:
>>               >Error in read.FCS(file.name <http://file.name>,
>> transformation =
>>         FALSE) : ' ' is not a valid
>>         file
>>         I then used the function:
>>               isFCSfile("cd cells_FMO 8_003.fcs")
>>         where cd cells_FMO 8_003.fcs is the name of the file. As expected
>> I
>>         obtained the
>>         following message:
>>               >cd cells_FMO 8_003.fcs FALSE
>>         meaning I reckon that the file is not a FCS. Since I am
>> completely new
>>         to this
>>         kind of analysis but I would not like to use flowJo, could
>> anybody tell
>>         me how
>>         to load the FCS files? In the rest of the file I am pasting the
>>         beginning of the
>>         cd cells_FMO 8_003.fcs file for further reference (I can't attach
>> the whole
>>         thing or even attaching the file because it is too big). From its
>>         gibberish I
>>         reckon that the encoding is probably wrong: I was expecting a
>> flatfile
>>         after all
>>         not ASCII. Would the problem be how the run was exported? FlowJo
>> however
>>         recognizes the files...
>>         Best regards,
>>         Luigi
>>
>>         ==============================
>>         FCS3.0         256    1927    1933 1192532 0 0
>>         $BEGINANALYSIS 0 $ENDANALYSIS 0 $BEGINSTEXT 0 $ENDSTEXT 0
>> $BEGINDATA 1933 $ENDDATA 1192532
>>         $FIL 180444.fcs $SYS Windows 7 6.1 $TOT 29765
>>         $PAR 10 $MODE L $BYTEORD 4,3,2,1 $DATATYPE F $NEXTDATA 0 CREATOR
>> BD
>>         FACSDiva
>>         Software Version 8.0 TUBE NAME FMO 8 $SRC cd
>>         cells EXPERIMENT
>>         NAME Experiment_001 GUID 4171c2f1-427b-4cc5-bf86-__39bb76803c48
>> $DATE 31-OCT-2014 $BTIM 16:07:12 $ETIM 16:09:25 SETTINGS Cytometer WINDOW
>>         EXTENSION 0.00 EXPORT USER NAME LuigiMarongiu EXPORT
>>         TIME 31-OCT-2014-16:07:11 FSC ASF 0.78 AUTOBS TRUE $INST
>>         $TIMESTEP 0.01 SPILL 3,405-450/50-A,405-655/8-A,__
>> 405-525/50-A,1,0.__0028442147740618787,0.__0923076944711957,0,1,0,0.__
>> 3425525014147933,0.__08630456626553264,1 APPLY
>>         COMPENSATION TRUE THRESHOLD FSC,5000 $P1N Time $P1R 262144 $P1B
>> 32 $P1E 0,0 $P1G 0.01 P1BS 0 P1MS 0 $P2N FSC-A $P2R 262144 $P2B 32 $P2E 0,0
>> $P2V 450 $P2G 1.0 P2DISPLAY LIN P2BS -1 P2MS 0 $P3N FSC-H $P3R 262144 $P3B
>> 32 $P3E 0,0 $P3V 450 $P3G 1.0 P3DISPLAY LIN P3BS -1 P3MS 0 $P4N FSC-W $P4R
>> 262144 $P4B 32 $P4E 0,0 $P4V 450 $P4G 1.0 P4BS -1 P4MS 0 $P5N SSC-A $P5R
>> 262144 $P5B 32 $P5E 0,0 $P5V 319 $P5G 1.0 P5DISPLAY LIN P5BS -1 P5MS 0 $P6N
>> SSC-H $P6R 262144 $P6B 32 $P6E 0,0 $P6V 319 $P6G 1.0 P6DISPLAY LIN P6BS -1
>> P6MS 0 $P7N SSC-W $P7R 262144 $P7B 32 $P7E 0,0 $P7V 319 $P7G 1.0 P7BS -1
>> P7MS 0 $P8N 405-450/50-A $P8S cd8
>>         - pac
>>         blue $P8R 262144 $P8B 32 $P8E 0,0 $P8V 450 $P8G 1.0 P8DISPLAY LOG
>> P8BS -1 P8MS 0 $P9N 405-655/8-A $P9S cd45ra
>>         -
>>         q655 $P9R 262144 $P9B 32 $P9E 0,0 $P9V 450 $P9G 1.0 P9DISPLAY LOG
>> P9BS -1 P9MS 0 $P10N 405-525/50-A $P10S ld
>>         -
>>         acqua $P10R 262144 $P10B 32 $P10E 0,0 $P10V 450 $P10G 1.0
>> P10DISPLAY LOG P10BS -1 P10MS 0 CST
>>         BEADS EXPIRED False      BHffEšùëGwI,E p F ÑgG„     F{¨
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>> ´
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>>
>>
>>
>>         ________________________________________________
>>         R-help at r-project.org <mailto:R-help at r-project.org> mailing list
>>         https://stat.ethz.ch/mailman/__listinfo/r-help
>>         <https://stat.ethz.ch/mailman/listinfo/r-help>
>>         PLEASE do read the posting guide
>>         http://www.R-project.org/__posting-guide.html
>>         <http://www.R-project.org/posting-guide.html>
>>         and provide commented, minimal, self-contained, reproducible code.
>>
>>
>>
>>     --
>>     Computational Biology / Fred Hutchinson Cancer Research Center
>>     1100 Fairview Ave. N.
>>     PO Box 19024 Seattle, WA 98109
>>
>>     Location: Arnold Building M1 B861
>>     Phone: (206) 667-2793 <tel:%28206%29%20667-2793>
>>
>>
>>     ______________________________________________
>>     R-help at r-project.org <mailto:R-help at r-project.org> mailing list
>>     https://stat.ethz.ch/mailman/listinfo/r-help
>>     PLEASE do read the posting guide http://www.R-project.org/
>> posting-guide.html
>>     and provide commented, minimal, self-contained, reproducible code.
>>
>>
>>
>
> --
> Computational Biology / Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N.
> PO Box 19024 Seattle, WA 98109
>
> Location: Arnold Building M1 B861
> Phone: (206) 667-2793
>

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