[R] Reading FCS files with flowCore package

William Dunlap wdunlap at tibco.com
Mon Nov 24 20:38:29 CET 2014


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      BHffEšùëGwI,E p F ÑgG„     F{¨
>> D˃×À G®CçË…BI33GAàõG¬ ‡G A G1ÊqGŒ
>> ƒG"  Bôk…Ab=pBÜ. BI33EÝ-ÂG ÊÀEÚ  Fe ×G h±Fc  DN
>> =ÀAë…C‰ÝqBK33FÀú G‚J F½– F VšG{ÚeF | B p¤Cb=pAÊ  BM33Gõ ÇG¡Ã’GÁö G³ôãGš
>> ;G•Œ
>> CÓ˜REY6 CiO\BO33EÑÞfGŠPlEÂ8 E l G€4.E 0 C p¤ÃHýqC!™šBQ33FKò G UùF6  F û
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>> BÅõÂBVÌÍF¥Ý£G®ÑdFrä G8•ÐG‘÷âG!Ý
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>> BhffFÜ
>> (GƒÂOFÕÆ F}v)G¡ù˜FHL BÃð¤Âb=pB9×
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>> CR {F $HB G®Bj  FÜé G“/ FÀ  G (ñGŒ  G Û B
>> ffG xRC ŒÍBlÌÍE× ×GŽ‡ EÁˆ E± …Gƒ» E¬  Àâ=pCtk…@ G®BnÌÍGœ›œG“c Gˆ
>> G/$;GŠë]G!` B¥£×Fš ŸBfG®BzffE³˜QG :zE € F0y G€µ›F/€
>> D€E Âþ… Cš‡®B{™šG“¨\G—)JGz  G,“ G‘ª¬G ¥ B k…G(ÊÔBÜ. B|ffG*<ðGŒÚ}G ´
>> F鈚G Ø8FÎ` AúzáƒLÍB  \B|ÌÍG¬}\G˜­ G œ€GY
>> G ‘ÕG@) C‰ÝqG p¶C n B~ÌÍFñ–3G“ïpFÑ  Fª ¤G‰ ŽFžà 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.
>
>

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