[R] Reading FCS files with flowCore package

Martin Morgan mtmorgan at fredhutch.org
Mon Nov 24 19:36:58 CET 2014 

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˃×ÀG®CçË…BI33GAàõG¬‡GA G1ÊqGŒ
> ƒG" Bôk…Ab=pBÜ.BI33EÝ-ÂGÊÀEÚ  Fe×Gh±Fc DN
> =ÀAë…C‰ÝqBK33FÀúG‚JF½– FVšG{ÚeF| Bp¤Cb=pAÊ  BM33GõÇG¡Ã’GÁö G³ôãGš;G•Œ
> CÓ˜REY6CiO\BO33EÑÞfGŠPlEÂ8 El G€4.E0 Cp¤ÃHýqC!™šBQ33FKòGUùF6  FûG†¾vF
> Â-¸RC0À ÂJ  BTffG^ùõGm at G5L GH—îGŠÏüG8ø Ap¤FœBÅõÂBVÌÍF¥Ý£G®ÑdFrä G8•ÐG‘÷âG!Ý
> C&¦fB—€ ÀG®BZ F„Ž®G„)~F€b F±ÕŠG´ôF ¢ Áâ=pB‡W
> B    \)B]33FøuáGŽ0ÏFߪ G¸.G‡E¤G
> Õ Bâ=pF0fB=áHB_™šEÇÙÂG…ÒdE¿( FRÙGˆ˜ÈFE” DgŠáÃ…C•záBa™šF×Õ£G¥ÌF¦Þ
> Fë¦HG¬:FÐ~ BøuÂC#ž¸BAë…BbÌÍGœa€G”G‡: G$ÛOG‹Ü¡Gà
> C#ž¸Fï“=BffBhffGŽß^G“í¾Gw@ G~GSFõ( BêQëFÕ¥…CW
> BhffFÜ
> (GƒÂOFÕÆ F}v)G¡ù˜FHL BÃð¤Âb=pB9×
> Bi™šG©MGœi0GŠŒ€GDžG“f·G*½ Bî\)C³Ç®CAë…Bj  G5[ðG™sûGG G]¾G‹ö!G3
> CR{F$HBG®Bj  FÜéG“/FÀ G(ñGŒGÛ B
> ffGxRCŒÍBlÌÍE××GŽ‡EÁˆ E±…Gƒ»E¬ Àâ=pCtk…@G®BnÌÍGœ›œG“cGˆ
> G/$;GŠë]G!` B¥£×FšŸBfG®BzffE³˜QG:zE € F0y G€µ›F/€
> D€EÂþ…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‰ÝqGp¶CnB~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

More information about the R-help mailing list