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]] > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@stat.math.ethz.ch > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > > > > [[alternative HTML version deleted]]