Raw Message

Message-ID: <54737ACA.8020809@fredhutch.org>
Date: 2014-11-24T18:36:58Z
From: Martin Morgan
Subject: Reading FCS files with flowCore package
In-Reply-To: <54733E1F.5050202@gmail.com>

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

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 <-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 = file.choose()

and selecting the file that you want to iniptu. Verify that the path is correct 
by displaying the result

   file.name

Martin

>      x <-read.FCS(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, 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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>
> ______________________________________________
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>


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