flowjo export/concatenate and flowCore
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Tiffany Chen ▴ 20
@tiffany-chen-3704
Last seen 7.3 years ago
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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@nishant-gopalakrishnan-3253
Last seen 7.3 years ago
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 at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >
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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]]
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