Message-ID: <547393B2.2000502@fredhutch.org>
Date: 2014-11-24T20:23:14Z
From: Martin Morgan
Subject: Reading FCS files with flowCore package
In-Reply-To: <CAF8bMcaZHJaRP3Ea44mBqDf=aopE=sJuud9SFx55wdhfabWwSg@mail.gmail.com>
On 11/24/2014 11:38 AM, William Dunlap wrote:
> 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
or to change the default to mustWork=TRUE, since there are not many use cases
for querying a non-existent system file?
(one irony I've stumbled across in my own code is to misspell 'mustWork', e.g.,
system.file("foo", mustwork=TRUE), which happily returns "").
Martin
> 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 <http://tibco.com>
>
> On Mon, Nov 24, 2014 at 10:36 AM, Martin Morgan <mtmorgan at fredhutch.org
> <mailto: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 <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 <http://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 <http://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 <http://file.name>
>
> Martin
>
> x <-read.FCS(file.name <http://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 <http://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 <mailto:R-help at r-project.org> mailing list
> https://stat.ethz.ch/mailman/__listinfo/r-help
> <https://stat.ethz.ch/mailman/listinfo/r-help>
> PLEASE do read the posting guide
> http://www.R-project.org/__posting-guide.html
> <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 <tel:%28206%29%20667-2793>
>
>
> ______________________________________________
> R-help at r-project.org <mailto: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