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
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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