[BioC] Newbie 'rflowcyt' question; problem loading facscan256.fcs

[Ulrik Stervbo]

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
> >
> > _______________________________________________
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> >
>
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Ulrik Stervbo
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Germany

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