Reading FCS files with flowCore package
Wrong list. See http://www.bioconductor.org/help/support/ --------------------------------------------------------------------------- Jeff Newmiller The ..... ..... Go Live... DCN:<jdnewmil at dcn.davis.ca.us> Basics: ##.#. ##.#. Live Go... Live: OO#.. Dead: OO#.. Playing Research Engineer (Solar/Batteries O.O#. #.O#. with /Software/Embedded Controllers) .OO#. .OO#. rocks...1k --------------------------------------------------------------------------- Sent from my phone. Please excuse my brevity.
On November 24, 2014 6:18:07 AM PST, Luigi <marongiu.luigi at gmail.com> wrote:
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 >
$TIMESTEP >0.01 >SPILL >3,405-450/50-A,405-655/8-A,405-525/50-A,1,0.0028442147740618787,0.0923076944711957,0,1,0,0.3425525014147933,0.08630456626553264,1 >APPLY
COMPENSATION >TRUE >THRESHOLD >FSC,5000 >$P1N >Time >$P1R >262144 >$P1B >32 >$P1E >0,0 >$P1G >0.01 >P1BS >0 >P1MS >0 >$P2N >FSC-A >$P2R >262144 >$P2B >32 >$P2E >0,0 >$P2V >450 >$P2G >1.0 >P2DISPLAY >LIN >P2BS >-1 >P2MS >0 >$P3N >FSC-H >$P3R >262144 >$P3B >32 >$P3E >0,0 >$P3V >450 >$P3G >1.0 >P3DISPLAY >LIN >P3BS >-1 >P3MS >0 >$P4N >FSC-W >$P4R >262144 >$P4B >32 >$P4E >0,0 >$P4V >450 >$P4G >1.0 >P4BS >-1 >P4MS >0 >$P5N >SSC-A >$P5R >262144 >$P5B >32 >$P5E >0,0 >$P5V >319 >$P5G >1.0 >P5DISPLAY >LIN >P5BS >-1 >P5MS >0 >$P6N >SSC-H >$P6R >262144 >$P6B >32 >$P6E >0,0 >$P6V >319 >$P6G >1.0 >P6DISPLAY >LIN >P6BS >-1 >P6MS >0 >$P7N >SSC-W >$P7R >262144 >$P7B >32 >$P7E >0,0 >$P7V >319 >$P7G >1.0 >P7BS >-1 >P7MS >0 >$P8N >405-450/50-A >$P8S >cd8
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blue >$P8R >262144 >$P8B >32 >$P8E >0,0 >$P8V >450 >$P8G >1.0 >P8DISPLAY >LOG >P8BS >-1 >P8MS >0 >$P9N >405-655/8-A >$P9S >cd45ra
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q655 >$P9R >262144 >$P9B >32 >$P9E >0,0 >$P9V >450 >$P9G >1.0 >P9DISPLAY >LOG >P9BS >-1 >P9MS >0 >$P10N >405-525/50-A >$P10S >ld
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