Re: [R] Reading FCS files with flowCore package

Mon, 24 Nov 2014 11:07:44 -0800 

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
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.






















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