[R] Reading FCS files with flowCore package

Luigi marongiu.luigi at gmail.com
Mon Nov 24 15:18:07 CET 2014 

Dear all,
I would like to use the R's Bioconductor package flowCore to do flow 
cytometry 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")
     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 
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