Reading FCS files with flowCore package

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

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
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