Question: Newbie 'rflowcyt' question; problem loading facscan256.fcs
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gravatar for Seth Falcon
13.5 years ago by
Seth Falcon7.4k
Seth Falcon7.4k 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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ADD COMMENTlink modified 13.5 years ago by Nolwenn LeMeur140 • written 13.5 years ago by Seth Falcon7.4k
Answer: Newbie 'rflowcyt' question; problem loading facscan256.fcs
0
gravatar for Nolwenn LeMeur
13.5 years ago by
Nolwenn LeMeur140 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 >
ADD COMMENTlink written 13.5 years ago by Nolwenn LeMeur140
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
ADD REPLYlink written 13.5 years ago by Ulrik Stervbo80
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