Message-ID: <FB6BBA13-3CCF-422D-8E7C-1450208D1350@dcn.davis.CA.us>
Date: 2014-11-24T19:27:46Z
From: Jeff Newmiller
Subject: Reading FCS files with flowCore package
In-Reply-To: <54733E1F.5050202@gmail.com>
Wrong list. See http://www.bioconductor.org/help/support/
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Jeff Newmiller The ..... ..... Go Live...
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Live: OO#.. Dead: OO#.. Playing
Research Engineer (Solar/Batteries O.O#. #.O#. with
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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
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>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?=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???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$HB?G?Bj F??
G?/F?
G(?G?G >? B
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??Bl??E??G???E?? E? >?G??E? ??=pCtk?@?G?Bn??G???G?c
G?
>G/$;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
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>
>etc.
>
>
>
>------------------------------------------------------------------------
>
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