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 <mtmor...@fredhutch.org <mailto:mtmor...@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 BHffEšùëGwI,E p F ÑgG„ F{¨ D˃×À G®CçË…BI33GAàõG¬ ‡G A G1ÊqGŒ ƒG" Bôk…Ab=pBÜ. 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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@r-project.org <mailto:R-help@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. 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-- 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@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.
