[BioC] flowjo export/concatenate and flowCore

[Nishant Gopalakrishnan]

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
>
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