[BioC] Error reading FCS file using FlowCore 1.6.0

[Florian Hahne]

Hi Noah,
got your file and it seems like there are two issues:
1.) No PnE keywords
2.) The offsets in the headers are incorrect. There is some redundancy 
in the FCS standard regarding where and how to store offsets, bitwidth 
and total event numbers, flowJo only gets the latter two right. The 
offsets are completely screwed and I guess they still point into the 
original data rather than the subset. Ugly!!!!

Anyways, the PnE problem can be overcome by setting transform=FALSE in 
read.FCS in which case we never get to the point where we need them (I 
love lazy evaluation...), the broken offsets needed a little patch. Just 
source the attached IO.R file and you should have an additional 
overrideHeader argument to read.FCS which you might want to set to TRUE 
for the messed up flowJo files. If set to FALSE you get the original 
behavior, i.e., offsets are read from the header and later we check 
whether the data we read in matches the recorded number of events.

I'll let Adam Treister know about this issue, should be a very simple 
fix ontheir side.

Florian



Noah Zimmerman 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
>


-- 
Florian Hahne, PhD
Computational Biology Program
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M2-B876
PO Box 19024
Seattle, Washington 98109-1024
206-667-3148
fhahne at fhcrc.org

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