Re: [R] Reading FCS files with flowCore package

Jeff Newmiller Mon, 24 Nov 2014 11:37:20 -0800

Wrong list. See http://www.bioconductor.org/help/support/
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Sent from my phone. Please excuse my brevity.


On November 24, 2014 6:18:07 AM PST, Luigi <marongiu.lu...@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>$P8S>cd8
>
>- pac 
>blue>$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
>
>- 
>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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>>P10DISPLAY>LOG>P10BS>-1>P10MS>0>CST
>
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>etc.
>
>
>
>------------------------------------------------------------------------
>
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Re: [R] Reading FCS files with flowCore package

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