There are a number of issues with floJo's export functionality  
creating invalid FCS files, but I didn't know this one until now. The  
PnE keywords are mandatory in an FCS file and the fact that they are  
missing means that most  other software has a problem reading these  
files. PnE encodes the amplification type used on the instrument  
(linear, log-scale) and I assume that the exported flowjo values have  
been transformed to accomodate for that. In this case setting PnE to  
linear is probably what flowJo should do, simply leaving out the  
keyword is very bad. I am reluctant to hardcore a fix in flowCore,  
there is a file standard for a good reason, but if you send me one  
example FCS file I can give you a patch so that you are at least able  
to read your data. I will also let Treestar know about this problem.

Florian


On 19.10mmerman" <noahz@stanford.edu> wrote:

> I receive the following error when I read a data file exported from  
> FlowJo
>
>
>
> > fcs1 <- read.FCS(file.name)
>
> Error in readFCSgetPar(x, paste("$P", 1:nrpar, "E", sep = "")) :
>
>   Parameter(s) $P1E not contained in 'x'Parameter(s) $P2E not  
> contained in 'x'Parameter(s) $P3E not contained in 'x'Parameter(s)  
> $P4E not contained in 'x'Parameter(s) $P5E not contained in  
> 'x'Parameter(s) $P6E not contained in 'x'Parameter(s) $P7E not  
> contained in 'x'Parameter(s) $P8E not contained in 'x'Parameter(s)  
> $P9E not contained in 'x'Parameter(s) $P10E not contained in  
> 'x'Parameter(s) $P11E not contained in 'x'Parameter(s) $P12E not  
> contained in 'x'Parameter(s) $P13E not contained in 'x'Parameter(s)  
> $P14E not contained in 'x'Parameter(s) $P15E not contained in  
> 'x'Parameter(s) $P16E not contained in 'x'Parameter(s) $P17E not  
> contained in 'x'Parameter(s) $P18E not contained in 'x'Parameter(s)  
> $P19E not contained in 'x'Parameter(s) $P20E not contained in  
> 'x'Parameter(s) $P21E not contained in 'x'Parameter(s) $P22E not  
> contained in 'x'Parameter(s) $P23E not contained in 'x'Parameter(s)  
> $P24E not contained in 'x'Parameter(s) $P25E not contained in  
> 'x'Parameter(s)
>
>
>
> The data has been analyzed in FlowJo by the researcher and exported  
> (after some preliminary gating) as described at http://www.flowjo.com/v6/html/export.html 
> . This error seems to originate from the function readFCSgetPar() in  
> IO.R which looks like it tries to do some matching of parameter  
> names. It is likely that the researcher performing the analysis had  
> already re-named the parameters to something more meaningful to her.  
> Would this cause this problem? Is there an easy workaround to this  
> problem that would allow me to read in this file?
>
>
>
> This is the second issue I’ve run into trying to move between FlowJo 
> -usable data files and flowCore data files. Sigh.
>
>
>
> Thank you in advance!
>
> Noah Zimmerman
>
>

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