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Ulrik Stervbo
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80
@ulrik-stervbo-1720
Last seen 10.2 years ago
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