Question: Newbie 'rflowcyt' question; problem loading facscan256.fcs
0
gravatar for Ulrik Stervbo
13.5 years ago by
Ulrik Stervbo80 wrote:
Hi Seth, Hi Nolwenn, I installed the latest rflowcyt, and get a different error: > fcs.loc <- system.file("fcs", package = "rfcdmin") > file.location <- paste(fcs.loc, "facscan256.fcs", sep = "/") > FC.FCSRobj <- read.FCS(file.location, UseS3 = TRUE, MY.DEBUG = TRUE,fcs.type = NULL) Start/Stop:$version [1] "FCS2.0" $TextStart [1] 256 $TextEnd [1] 1595 $TextLength [1] 1340 $DataStart [1] 1792 $DataEnd [1] 51791 $DataLength [1] 50000 $AnalysisStart [1] 0 $AnalysisEnd [1] 0 Error in 1:last.pos.delim : result would be too long a vector In addition: Warning messages: 1: no non-missing arguments to max; returning -Inf 2: Metadata Length Discrepancy: TextLength = 1340 but valid metadata length = -Inf in: read.FCS(file.location, UseS3 = TRUE, MY.DEBUG = TRUE, fcs.type = NULL) 3: The metadata will be truncated up to the last delimiter. in: read.FCS(file.location, UseS3 = TRUE, MY.DEBUG = TRUE, fcs.type = NULL) The result form library(help=rflowcyt): Information on package 'rflowcyt' Description: Package: rflowcyt Version: 1.5.2 Date: 2006-05-27 Title: Statistical tools and data structures for analytic flow cytometry Author: A.J. Rossini, J.Y. Wan, N. Le Meur and Zoe Moodie Maintainer: N. Le Meur <nlemeur at="" fhcrc.org=""> Depends: R (>= 2.3.0), survival, xtable, stats, KernSmooth, MASS,grid, splancs, methods, hexbin, rfcdmin (>= 0.9.0), fields, lattice,locfit Imports: prada,graphics Suggests: xgobi Description: Provides basic S4 data structures and routines for analysing flow cytometry data. License: GNU General Public License 2.0. URL: http://www.analytics.washington.edu/downloads/rflowcyt/ biocViews: Statistics, Infrastructure, CellBasedAssays Packaged: Sun May 28 05:37:33 2006; biocbuild Built: R 2.3.0; ; 2006-05-31 17:17:31; unix And from search > search() [1] ".GlobalEnv" "package:digest" "package:rflowcyt" [4] "package:locfit" "package:akima" "package:fields" [7] "package:rfcdmin" "package:hexbin" "package:colorspace" [10] "package:lattice" "package:splancs" "package:sp" [13] "package:grid" "package:MASS" "package:KernSmooth" [16] "package:xtable" "package:survival" "package:splines" [19] "package:methods" "package:stats" "package:graphics" [22] "package:grDevices" "package:utils" "package:datasets" [25] "Autoloads" "package:base" I havent yet been able to download R to a windows computer. Ulrik On 5/30/06, Ulrik Stervbo <ulriks at="" ruc.dk=""> wrote: > Hi Seth, Hi Nolwenn > > I get the same signature as well: > > library("digest") > > dataFile <- system.file("fcs/facscan256.fcs", package="rfcdmin") > > dataFile > [1] "/usr/lib/R/library/rfcdmin/fcs/facscan256.fcs" > > digest(dataFile, file=TRUE) > [1] "bfc603037460c0023569159c7360be0c" > > I have not yet tried to load my own datafiles, mainly because I am not > really sure how. Performing the few examples in the prada package > works without problems (but then again the readFCS methods are > probably not the same) > > I have been wanting to see if I could reproduce the error on windows. > However, that as well as testing the new lib may be a few days, since > other things (laboratory work) are demanding my attention. > > I will get back with the results as soon as they get in. > > Thanks > Ulrik > > On 5/29/06, Nolwenn LeMeur <nlemeur at="" fhcrc.org=""> wrote: > > Hi Seth, Hi Ulrik, > > > > I have verified the md5 hash of the data file on my system and I get the > > same signature as Seth: > > > > > library("digest") > > > datafile=system.file("fcs/facscan256.fcs",package="rfcdmin") > > > digest(datafile,file=TRUE) > > [1] "bfc603037460c0023569159c7360be0c" > > > > > > > > Nolwenn > > > > *********************************** > > Nolwenn Le Meur, PhD > > Fred Hutchinson Cancer Research Center > > Computational Biology > > 1100 Fairview Ave. N., M2-B876 > > P.O. Box 19024 > > Seattle, WA 98109-1024 > > > > On Mon, 29 May 2006, Seth Falcon wrote: > > > > > Nolwenn LeMeur <nlemeur at="" fhcrc.org=""> writes: > > > > Hi Ulrik, > > > > > > > > I was not able to reproduce your error. > > > > > > I wonder if everyone is using the exact same dataset? > > > > > > > Ulrik Stervbo wrote: > > > >>Here's what I've done after starting R: > > > >> > > > >> > > > >>>library(rflowcyt) > > > >>>library(Biobase) > > > >>>fcs.loc <- system.file("fcs", package = "rfcdmin") > > > >>>file.location <- paste(fcs.loc, "facscan256.fcs", sep = "/") > > > >>>FC.FCSRobj <- read.FCS(file.location, UseS3 = TRUE, MY.DEBUG = > > > >>>TRUE,fcs.type = NULL) > > > > > > Here's one way to verify: > > > > > > 1. Install the digest package. From R, do: > > > > > > source("http://bioconductor.org/biocLite.R") > > > biocLite("digest") > > > > > > 2. Obtain the md5 hash of the data file. By comparing this output, > > > we'll know whether everyone has the same file to begin with. > > > > > > library("rflowcyt") > > > library("digest") > > > > > > ## Get the path to the data file: > > > dataFile <- system.file("fcs/facscan256.fcs", package="rfcdmin") > > > > dataFile > > > [1] "/Users/seth/RLIB-2.4/rfcdmin/fcs/facscan256.fcs" > > > > > > ## Compute the md5 hash of the file, you should get the _same_ > > > ## string as I do here. If not, we have different files. > > > > digest(dataFile, file=TRUE) > > > [1] "bfc603037460c0023569159c7360be0c" > > > > > > + seth > > > > > > _______________________________________________ > > > Bioconductor mailing list > > > Bioconductor at stat.math.ethz.ch > > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > > > > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor at stat.math.ethz.ch > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > > > > > -- > Ulrik Stervbo > Cantianstrasse 23 > 10437 Berlin > Germany > > Home: +49 30 441 12 81 > Handy: +49 178 145 82 31 > Blog: http://ulrikstervbo.blogspot.com > Mailing-list: http://www.coollist.com/group.cgi?l=ulrik_i_berlin > -- Ulrik Stervbo Cantianstrasse 23 10437 Berlin Germany Home: +49 30 441 12 81 Handy: +49 178 145 82 31 Blog: http://ulrikstervbo.blogspot.com Mailing-list: http://www.coollist.com/group.cgi?l=ulrik_i_berlin
ADD COMMENTlink modified 13.5 years ago by Seth Falcon7.4k • written 13.5 years ago by Ulrik Stervbo80
Answer: Newbie 'rflowcyt' question; problem loading facscan256.fcs
0
gravatar for Seth Falcon
13.5 years ago by
Seth Falcon7.4k
Seth Falcon7.4k wrote:
"Ulrik Stervbo" <ulriks at="" ruc.dk=""> writes: > I installed the latest rflowcyt, and get a different error: What does R say for: > Sys.getlocale() [1] "C" Just a guess, but perhaps there is a character encoding issue here. > The result form library(help=rflowcyt): A more concise and much more useful way to summarize is to include the output of: sessionInfo() This will report your R version, platform, and versions of loaded packages. + seth
ADD COMMENTlink written 13.5 years ago by Seth Falcon7.4k
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