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

[Seth Falcon]

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