[R] Reading FCS files with flowCore package

Martin Morgan mtmorgan at fredhutch.org
Mon Nov 24 21:23:14 CET 2014 

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
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>
>         ________________________________________________
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>     --
>     Computational Biology / Fred Hutchinson Cancer Research Center
>     1100 Fairview Ave. N.
>     PO Box 19024 Seattle, WA 98109
>
>     Location: Arnold Building M1 B861
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>     ______________________________________________
>     R-help at r-project.org <mailto:R-help at r-project.org> mailing list
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>     PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
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-- 
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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