[BioC] iFlow error in opening FCS and LMD files

[Josef Spidlen]

Hi Anna,
have you tried simply reading the file in R with flowCore?

library(flowCore)
x <- read.FCS('path to your LMS file')

Do you get an error message or can you read it? As far as I know, an LMD 
file is just a list mode FCS file; we have some of these generated from 
Coulter's Cytomics FC500. These files sometimes cause problems in 
different software since they are unusual in terms of commonly 
containing more than 1 data set within the file. This is legal in FCS 
but I have also seen some missing offset information in these files in 
the FCS header segment, which is not FCS compliant (however, the 
appropriate information can sometimes still be derived from info in the 
text segment). TreeStar guys put a lot of effort into reading basically 
all the files out there so if a file is successfully read in FlowJo does 
not really tell you whether the file is OK or not.

If you want, you can send me one of the files offline and I can have a 
closer look at it.

Cheers,
Josef


> ------------------------------
>
> Message: 2
> Date: Fri, 6 Aug 2010 11:50:15 -0400
> From: Anna Dvorkin<dvorkin at mcmaster.ca>
> To: bioconductor at stat.math.ethz.ch
> Subject: [BioC] iFlow error in opening FCS and LMD files
> Message-ID:
>          <AANLkTik1K40KSBf5P6xDqBQ1FFVgL3QA-LjmM8_wS1f8 at mail.gmail.com>
> Content-Type: text/plain
>
> Dear All,
>
> I have been trying to analyze files I obtained from a flow cytometer. In
> order to do that I am trying to use the iFlow package.
>
>
> After I write the following:
> *library(iFlow)*
>
> A GUI window opens and I choose the files I want to analyse.
> However, after I click on "Open" in the GUI, I receive the following
> message:
>
> *"Error: '.SigArgs' is shorter than '.SigLength' says it should be"*
> After I close that window, I can see, that the following packages were
> successfully loaded:
>
> *Loading required package: RGtk2
> Loading required package: flowViz
> Loading required package: lattice
> KernSmooth 2.23 loaded
> Copyright M. P. Wand 1997-2009
> Loading required package: flowStats
> Loading required package: fda
> Loading required package: splines
> Loading required package: zoo
> Loading required package: mvoutlier
> Loading required package: cluster*
>
> I tried two analyze two different types of files: LMD and FCS. All files are
> ok, since I could analyze
> them in FlowJo, however, I cannot analyze them with iFlow.
>
> Can anybody, please, explain to me what am I doing wrong?
>
> Thank you very much!
> Regards,
> Anna
>
>
>
> --
> Anna Dvorkin, Ph.D.
> Department of Biochemistry and Biomedical Sciences
> McMaster University
> 1200 Main Street West
> Hamilton, ON L8N
> Canada
> E-mail:    dvorkin at mcmaster.ca
>
>          [[alternative HTML version deleted]]
>
>    

-- 
Josef Spidlen, Ph.D.
Terry Fox Laboratory, BC Cancer Agency
675 West 10th Avenue, V5Z 1L3 Vancouver, BC, Canada

Tel: +1 (604) 675-8000 x 7755
http://www.terryfoxlab.ca/people/rbrinkman/josef.aspx