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Luigi

2014-Nov-24 14:18 UTC

[R] Reading FCS files with flowCore package

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 
$BEGINANALYSIS0$ENDANALYSIS0$BEGINSTEXT0$ENDSTEXT0$BEGINDATA1933$ENDDATA1192532 
$FIL180444.fcs$SYSWindows 7 6.1$TOT29765 
$PAR10$MODEL$BYTEORD4,3,2,1$DATATYPEF$NEXTDATA0CREATORBD 
FACSDiva Software Version 8.0TUBE 
NAMEFMO 8$SRCcd cellsEXPERIMENT 
NAMEExperiment_001GUID4171c2f1-427b-4cc5-bf86-39bb76803c48$DATE31-OCT-2014$BTIM16:07:12$ETIM16:09:25SETTINGSCytometerWINDOW
EXTENSION0.00EXPORT USER NAMELuigiMarongiuEXPORT 
TIME31-OCT-2014-16:07:11FSC ASF0.78AUTOBSTRUE$INST 
$TIMESTEP0.01SPILL3,405-450/50-A,405-655/8-A,405-525/50-A,1,0.0028442147740618787,0.0923076944711957,0,1,0,0.3425525014147933,0.08630456626553264,1APPLY
COMPENSATIONTRUETHRESHOLDFSC,5000$P1NTime$P1R262144$P1B32$P1E0,0$P1G0.01P1BS0P1MS0$P2NFSC-A$P2R262144$P2B32$P2E0,0$P2V450$P2G1.0P2DISPLAYLINP2BS-1P2MS0$P3NFSC-H$P3R262144$P3B32$P3E0,0$P3V450$P3G1.0P3DISPLAYLINP3BS-1P3MS0$P4NFSC-W$P4R262144$P4B32$P4E0,0$P4V450$P4G1.0P4BS-1P4MS0$P5NSSC-A$P5R262144$P5B32$P5E0,0$P5V319$P5G1.0P5DISPLAYLINP5BS-1P5MS0$P6NSSC-H$P6R262144$P6B32$P6E0,0$P6V319$P6G1.0P6DISPLAYLINP6BS-1P6MS0$P7NSSC-W$P7R262144$P7B32$P7E0,0$P7V319$P7G1.0P7BS-1P7MS0$P8N405-450/50-A$P8Scd8
- pac 
blue$P8R262144$P8B32$P8E0,0$P8V450$P8G1.0P8DISPLAYLOGP8BS-1P8MS0$P9N405-655/8-A$P9Scd45ra
- 
q655$P9R262144$P9B32$P9E0,0$P9V450$P9G1.0P9DISPLAYLOGP9BS-1P9MS0$P10N405-525/50-A$P10Sld
- 
acqua$P10R262144$P10B32$P10E0,0$P10V450$P10G1.0P10DISPLAYLOGP10BS-1P10MS0CST 
BEADS EXPIREDFalse     BHffE???GwI,E p F??gG?    F{? 
D????G?C???BI33GA??G??GA G1?qG?
?G"? B?k?Ab=pB?.BI33E?-?G???E?  Fe??G?h?Fc DN
=?A??C??qBK33F??G?JF?? FV?G{?eF| Bp?Cb=pA?  BM33G??G???G?? 
G???G?;G?? C??REY6?CiO\BO33E??fG?PlE?8 El G?4.E0 
Cp??H?qC!??BQ33FK?G?U?F6  F?G??vF  ?-?RC0? ?J  BTffG^??G?m at G5L 
GH??G???G8? Ap?F??B???BV??F???G??dFr? G8??G???G!? C&?fB?? ??G?BZ  
F???G?)~F?b F???G???F ? ??=pB?W
B    \)B]33F?u?G?0?F?? G?.G?E?G
? B?=pF0fB=?HB_??E???G??dE?( FR?G???FE? Dg????C?z?Ba??F???G???F?? 
F??HG??:F?~ B?u?C#??BA??Bb??G?a?G?G?: G$?OG???G? 
C#??F??=B?ffBhffG??^G???Gw@ G~G?SF?( B?Q?F???CW
BhffF?
(G??OF?? F}v)G???FHL B????b=pB9?
Bi??G?MG?i0G???GD?G?f?G*? B?\)C???CA??Bj  G5[?G?s?GG 
G]?G??!G3 CR{F$HB?G?Bj  F??G?/F? G(?G?G? B
ffGxRC??Bl??E??G???E?? E??G??E? ??=pCtk?@?G?Bn??G???G?cG? 
G/$;G??]G!` B???F??BfG?BzffE??QG?:zE ? F0y G???F/? 
D?E???C???B{??G??\G?)JGz G,?G???G? B?k?G(??B?.B|ffG*<?G??}G? 
F???G??8F?` A?z???L?B?\B|??G?}\G??G???GY
G???G@) C??qGp?CnB~??F??3G??pF? F??G??F?? C?G?F9

etc.

Martin Morgan

2014-Nov-24 18:36 UTC

head link

[R] Reading FCS files with flowCore package

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
>
$BEGINANALYSIS0$ENDANALYSIS0$BEGINSTEXT0$ENDSTEXT0$BEGINDATA1933$ENDDATA1192532
> $FIL180444.fcs$SYSWindows 7 6.1$TOT29765
> $PAR10$MODEL$BYTEORD4,3,2,1$DATATYPEF$NEXTDATA0CREATORBD FACSDiva
> Software Version 8.0TUBE NAMEFMO 8$SRCcd
> cellsEXPERIMENT
>
NAMEExperiment_001GUID4171c2f1-427b-4cc5-bf86-39bb76803c48$DATE31-OCT-2014$BTIM16:07:12$ETIM16:09:25SETTINGSCytometerWINDOW
> EXTENSION0.00EXPORT USER NAMELuigiMarongiuEXPORT
> TIME31-OCT-2014-16:07:11FSC ASF0.78AUTOBSTRUE$INST
>
$TIMESTEP0.01SPILL3,405-450/50-A,405-655/8-A,405-525/50-A,1,0.0028442147740618787,0.0923076944711957,0,1,0,0.3425525014147933,0.08630456626553264,1APPLY
>
COMPENSATIONTRUETHRESHOLDFSC,5000$P1NTime$P1R262144$P1B32$P1E0,0$P1G0.01P1BS0P1MS0$P2NFSC-A$P2R262144$P2B32$P2E0,0$P2V450$P2G1.0P2DISPLAYLINP2BS-1P2MS0$P3NFSC-H$P3R262144$P3B32$P3E0,0$P3V450$P3G1.0P3DISPLAYLINP3BS-1P3MS0$P4NFSC-W$P4R262144$P4B32$P4E0,0$P4V450$P4G1.0P4BS-1P4MS0$P5NSSC-A$P5R262144$P5B32$P5E0,0$P5V319$P5G1.0P5DISPLAYLINP5BS-1P5MS0$P6NSSC-H$P6R262144$P6B32$P6E0,0$P6V319$P6G1.0P6DISPLAYLINP6BS-1P6MS0$P7NSSC-W$P7R262144$P7B32$P7E0,0$P7V319$P7G1.0P7BS-1P7MS0$P8N405-450/50-A$P8Scd8
> - pac
>
blue$P8R262144$P8B32$P8E0,0$P8V450$P8G1.0P8DISPLAYLOGP8BS-1P8MS0$P9N405-655/8-A$P9Scd45ra
> -
>
q655$P9R262144$P9B32$P9E0,0$P9V450$P9G1.0P9DISPLAYLOGP9BS-1P9MS0$P10N405-525/50-A$P10Sld
> -
>
acqua$P10R262144$P10B32$P10E0,0$P10V450$P10G1.0P10DISPLAYLOGP10BS-1P10MS0CST
> BEADS EXPIREDFalse     BHffE???GwI,E p F??gG?    F{?
> D????G?C???BI33GA??G??GA G1?qG?
> ?G"? B?k?Ab=pB?.BI33E?-?G???E?  Fe??G?h?Fc DN
> =?A??C??qBK33F??G?JF?? FV?G{?eF| Bp?Cb=pA?  BM33G??G???G?? G???G?;G??
> C??REY6?CiO\BO33E??fG?PlE?8 El G?4.E0 Cp??H?qC!??BQ33FK?G?U?F6  F?G??vF
> ?-?RC0? ?J  BTffG^??G?m at G5L GH??G???G8? Ap?F??B???BV??F???G??dFr?
G8??G???G!?
> C&?fB?? ??G?BZ F???G?)~F?b F???G???F ? ??=pB?W
> B    \)B]33F?u?G?0?F?? G?.G?E?G
> ? B?=pF0fB=?HB_??E???G??dE?( FR?G???FE? Dg????C?z?Ba??F???G???F??
> F??HG??:F?~ B?u?C#??BA??Bb??G?a?G?G?: G$?OG???G?
> C#??F??=B?ffBhffG??^G???Gw@ G~G?SF?( B?Q?F???CW
> BhffF?
> (G??OF?? F}v)G???FHL B????b=pB9?
> Bi??G?MG?i0G???GD?G?f?G*? B?\)C???CA??Bj  G5[?G?s?GG G]?G??!G3
> CR{F$HB?G?Bj  F??G?/F? G(?G?G? B
> ffGxRC??Bl??E??G???E?? E??G??E? ??=pCtk?@?G?Bn??G???G?cG?
> G/$;G??]G!` B???F??BfG?BzffE??QG?:zE ? F0y G???F/?
> D?E???C???B{??G??\G?)JGz G,?G???G? B?k?G(??B?.B|ffG*<?G??}G?
> F???G??8F?` A?z???L?B?\B|??G?}\G??G???GY
> G???G@) C??qGp?CnB~??F??3G??pF? F??G??F?? C?G?F9
>
> etc.
>
>
>
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>

-- 
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109

Location: Arnold Building M1 B861
Phone: (206) 667-2793

Jeff Newmiller

2014-Nov-24 19:27 UTC

head link

[R] 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>$P8S>cd8
>
>- pac 
>blue>$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>$P10S>ld
>
>- 
>acqua>$P10R>262144>$P10B>32>$P10E>0,0>$P10V>450>$P10G>1.0>P10DISPLAY>LOG>P10BS>-1>P10MS>0>CST
>
>BEADS EXPIRED>False>     BHffE???GwI,E p F??gG?    F{? 
>D????G?C???BI33GA??G??GA G1?qG?
>?G"? B?k?Ab=pB?.BI33E?-?G???E?  Fe??G?h?Fc DN
>=?A??C??qBK33F??G?JF?? FV?G{?eF| Bp?Cb=pA?  BM33G??G???G?? 
>G???G?;G?? C??REY6?CiO\BO33E??fG?PlE?8 El G?4.E0 
>Cp??H?qC!??BQ33FK?G?U?F6  F?G??vF  ?-?RC0? ?J  BTffG^??G?m at G5L 
>GH??G???G8? Ap?F??B???BV??F???G??dFr? G8??G???G!? C&?fB?? ??G?BZ  
>F???G?)~F?b F???G???F ? ??=pB?W
>B    \)B]33F?u?G?0?F?? G?.G?E?G
>? B?=pF0fB=?HB_??E???G??dE?( FR?G???FE? Dg????C?z?Ba??F???G???F??
>F??HG??:F?~ B?u?C#??BA??Bb??G?a?G?G?: G$?OG???G? 
>C#??F??=B?ffBhffG??^G???Gw@ G~G?SF?( B?Q?F???CW
>BhffF?
>(G??OF?? F}v)G???FHL B????b=pB9?
>Bi??G?MG?i0G???GD?G?f?G*? B?\)C???CA??Bj  G5[?G?s?GG 
>G]?G??!G3 CR{F$HB?G?Bj  F??G?/F?
 G(?G?G>? B>ffGxRC??Bl??E??G???E?? E?>?G??E? ??=pCtk?@?G?Bn??G???G?c
G? >G/$;G??]G!` B???F?
?BfG?BzffE??QG?:zE ? F0y G???F/? >D?E???C???B{??G??\G?)JGz G,?
G???G? B?k?G(??B?.B|ffG*<?G??}G? >F???G??8F?` A?z???L?B
?\B|??G?}\G??G???GY>G???G@) C??qGp?CnB~??F??3G??pF? F??G??F?? C?G?F9
>
>etc.
>
>
>
>------------------------------------------------------------------------
>
>______________________________________________
>R-help at r-project.org mailing list
>https://stat.ethz.ch/mailman/listinfo/r-help
>PLEASE do read the posting guide
>http://www.R-project.org/posting-guide.html
>and provide commented, minimal, self-contained, reproducible code.

William Dunlap

2014-Nov-24 19:38 UTC

head link

[R] Reading FCS files with flowCore package

If help files used the mustWork=TRUE argument to system.file() this sort of
problem
would become more apparent to the user.  It would give a clear error
message from
system.file() instead of a mysterious error about file "" not being
valid
or, worse, a hang
from an input command waiting for the user to type something into standard
input (because
scan() and others treat file="" the same as scan=stdin()).

Bill Dunlap
TIBCO Software
wdunlap tibco.com

On Mon, Nov 24, 2014 at 10:36 AM, Martin Morgan <mtmorgan at
fredhutch.org>
wrote:
> 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
>> 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
>> -
>> acqua $P10R 262144 $P10B 32 $P10E 0,0 $P10V 450 $P10G 1.0 P10DISPLAY
LOG
>> P10BS -1 P10MS 0 CST
>> BEADS EXPIRED False      BHffE???GwI,E p F ?gG?     F{?
>> D???? G?C???BI33GA??G? ?G A G1?qG?
>> ?G"  B?k?Ab=pB?. BI33E?-?G ??E?  Fe ?G h?Fc  DN
>> =?A??C??qBK33F?? G?J F?? F V?G{?eF | B p?Cb=pA?  BM33G? ?G???G?? G???G?
>> ;G??
>> C??REY6 CiO\BO33E??fG?PlE?8 E l G?4.E 0 C p??H?qC!??BQ33FK? G U?F6  F ?
>> G??vF ?-?RC0? ?J  BTffG^??G m at G5L GH??G???G8? A p?F ?
>> B???BV??F???G??dFr? G8??G???G!?
>> C&?fB?? ? G?BZ F???G?)~F?b F???G ??F ? ??=pB?W
>> B    \)B]33F?u?G?0?F?? G ?.G?E?G
>> ? B?=pF0 fB=?HB_??E???G??dE?( FR? G???FE? Dg??? ? C?z?Ba??F???G? ?F??
>> F??HG ?:F?~ B?u?C#??BA??Bb??G?a?G?  G?: G$?OG???G ?
>> C#??F??=B ffBhffG??^G???Gw@ G  ~G  SF?( B?Q?F???C W
>> BhffF?
>> (G??OF?? F}v)G???FHL B????b=pB9?
>> Bi??G?M G?i0G???GD? G?f?G*? B?\)C???CA??Bj  G5[?G?s?G G G ]?G??!G 3
>> CR {F $HB G?Bj  F?? G?/ F?  G (?G?  G ? B
>> ffG xRC ??Bl??E? ?G?? E?? E? ?G?? E?  ??=pCtk?@ G?Bn??G???G?c G?
>> G/$;G??]G!` B???F? ?BfG?BzffE??QG :zE ? F0y G???F/?
>> D?E ??? C???B{??G??\G?)JGz  G,? G???G ? B k?G(??B?. B|ffG*<?G??}G ?
>> F???G ?8F?` A?z???L?B  \B|??G?}\G?? G ??GY
>> G ??G@) C??qG p?C n B~??F??3G??pF?  F? ?G? ?F?? C G?F9
>>
>> etc.
>>
>>
>>
>> ______________________________________________
>> R-help at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-help
>> PLEASE do read the posting guide http://www.R-project.org/
>> posting-guide.html
>> and provide commented, minimal, self-contained, reproducible code.
>>
>>
>
> --
> Computational Biology / Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N.
> PO Box 19024 Seattle, WA 98109
>
> Location: Arnold Building M1 B861
> Phone: (206) 667-2793
>
>
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>
>
	[[alternative HTML version deleted]]

R help - Nov 2014 - Reading FCS files with flowCore package

[R] Reading FCS files with flowCore package

[R] Reading FCS files with flowCore package

[R] Reading FCS files with flowCore package

[R] Reading FCS files with flowCore package