Hi Nishant,
The tips you gave me look like they will work, and I will try them.
Importing the aggregate text file and calling the constructor will best meet
my needs, because there seem to be different header & formatting issues
depending on how i export files from flowjo. Thank you so much, I'm new to
flowCore.

You are correct about the purpose of the concatenate function.  The
export/concatenate function in flowJo has two functions, (1) to export
whatever files you have chosen, (2) to export these files as one, combined
fcs file.

Once again, I really appreciate your help! Thanks for the quick response.

Cheers,
~Tiffany


On Thu, Sep 24, 2009 at 10:51 AM, Nishant Gopalakrishnan <ngopalak@fhcrc.org
> wrote:

> Hi Tiffany,
>
> What exactly does the concatenate function in flowJO do ?.
>
> If the function is  indeed combining two files and the problem is
> created by a mis formatted header  created by the concatenate function,
> would it not be possible to export them as single FCS files from flowJo
> and then combine them in flowCore ?.
>
> It is possible to create flowFrame objects using  the constructor for
> flowFrame, if you were to read in the matrix from a txt file
> (using read.csv or read.delim   etc.) into the exprs slot  and supply
> the appropriate arguments for the parameters
> and description slots.
>
> ‘ new("flowFrame",’
>     ‘ exprs = ...., Object of class matrix’
>     ‘ parameters = ...., Object of class AnnotatedDataFrame’
>     ‘ description = ...., Object of class list’
>     ‘ )’
>
>
> Nishant
>
> Tiffany Chen wrote:
> > Hello List,
> > I've noticed some recent problems with file formatting exported from
> flowjo
> > with the concatenate function. I did some searching and found that this
> was
> > a recent feature, and unfortunately I am unable to import my concatenated
> > files into flowCore.
> >
> > In short, header files are strangely broken between the point when they
> come
> > out of "concatenate" from flowjo and are read into flowCore.
> >
> > temp <- read.FCS('myfile.fcs')
> > Error in readFCSgetPar(x, "$BYTEORD") :
> >   Parameter(s) $BYTEORD not contained in 'x'
> >
> > I tried the fix posted previously for reading flowjo outputted files, but
> i
> > think this may be a different case. Opening the file in a basic text
> editor
> > shows some different formatting issues that may or may not be causing
> this
> > problem.
> >
> > Sadly, I need to analyze the combination of these files, and not the
> > individual files alone, hence the use of the "concatenate" function.
> >
> > My questions are as follow:
> >
> > (1) is it possible to read a text file (data only) as a flowSet? As a
> result
> > I could bypass the header errors from flowjo and just use my combined
> > dataset.
> > (2) does this issue pop up with anyone else? I submitted a ticket to
> flowjo,
> > but i would prefer to be able to analyze my combined data in flowCore
> asap
> > :)
> >
> > Thanks to anyone who has any input on this matter!
> >
> > Cheers,
> > ~Tiffany Chen
> >
> >       [[alternative HTML version deleted]]
> >
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> >
>
>

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