plantarum/flowploidy

An R package for flow cytometry histogram analysis

flowploidy's Issues

issue with installation

after following the installation procedure (stable) I get the following error when I try to load the library:
Error: package or namespace load failed for ‘flowPloidy’ in rbind(info, getNamespaceInfo(env, "S3methods")):
number of columns of matrices must match (see arg 2)

I tried to remove and reinstall the package without any change. Thanks for your help.
Alex

Problem importing files in development version of flowPloidy

Hi,

Recently I saw that you added a new feature in the development version of flowPloidy to asses endopolyploidy. This would be very useful for my research, as my samples contain not only diploid and tetraploid cells, but also hexaploid and octaploid cells. I want to asses the fraction of polyploid cells in my samples, so I would like to asses every peak like a separate group of cells.
After I installed flowPloidy from the GitHub repository, I tried including the G2 = FALSE argument in the batchFlowHist function, but I get an error: "**PROBLEM: I couldn't import ..... .LMD **The following files failed to load:....LMD". There is no further explanation of why these files do not load. When I don't include the G2 = FALSE argument, I can analyse the same files perfectly with the stable flowPloidy version.

Do you know a way to load my files so I can assess endopolyploidy with the development version?

Thanks for your help.

Iris

function batchFH picks GUID as main instead of file name

Hi! I'm having trouble getting the main label of the histogram. It is a long GUID but not the file name. Any suggestions if I can add an argument in batchFlowHist ( ) . full.names =TRUE, alter.names=FALSE didn't work.
With thanks
Abhi

Will flowPloidy work on mammalian samples?

Hi - I am really impressed with the ease of use of this tool, so thanks for your hard work! My present issue is that I am having some issues when using flowPloidy to analyze human cancer cell lines DNA content (measured via propidium iodide fluorescence). I'm a bit confused about how the model finds the location of the G2 peak, because I am not able to generate a model that accurately picks this peaks from my data, although it does come close. I've attached an image showing that the G1 peak is correctly modeled in both height and location, but the S phase and G2 peak in the model seem to be shifted to the right. Do you have any suggestions on how I might better model my data? Or is this the expected behavior? Thanks!

Histogram bins setting error with files from CytExpert software

Hi Tyler! Thanks for making this package, it is a pleasure to use it! I am not sure if my issue is related to flowPloidy alone, but maybe you could try to help?

CytExpert software at my lab sometimes produces FCS files that can be read with read.FCS but fail to pass through FlowHist in some channels. My humble effort in debugging led to realisation that the error comes from setBins function. The error reads as follows:

> FlowHist("sas.fcs", "FL2.H")
Error in if (xx >= first.channel & xx < length(intensity)) { : 
  missing value where TRUE/FALSE needed

I attach the minimal FCS file that causes the error, it has only 6 events in it. Is there anything I (or you?) could do about it?

Cheers,
Nikita

File: sas.fcs.zip