Bugs in statistics and plot formatting

[Anonymous]

Hej Sven,

I was looking for a FCS analyzer for Ubuntu and ended up with your program which is the only one running so far, so very nice job! Now I encountered at least two bugs: 1. I can not calculate any statistics. The Program throws an error on the command line but will do nothing in the gui:

Exception in thread "AWT-EventQueue-0" java.lang.NoSuchMethodError: java.util.ArrayList.sort(Ljava/util/Comparator;)V
    at FCSalyzer.FCS.FCS_statistics$statHolder.calculateStats(FCS_statistics.java:454)
    at FCSalyzer.FCS.FCS_statistics$statHolder.access$200(FCS_statistics.java:404)
    at FCSalyzer.FCS.FCS_statistics.calculateBasics(FCS_statistics.java:269)
    at FCSalyzer.FCS.FCS_statistics.<init>(FCS_statistics.java:179)
    at [...]

The second thing I noticed is the missing plotting function in histograms. If I gate a population of cells in a dotplot and want to see the histgram of that gate, the histogram will not respond and simply plot the whole data set. I hope that helps for your development. Would be great if I could use the program for my next paper ;-).

Jan

[Sven Mostböck]

Hej Jan,

thanks for your message. I am glad to hear that FCSalyzer may become useful for you. I chose Java especially to make it runnable on many different OS.

Now about your two bugs:
Yes, the histogram plots were not properly updated. This bug has been repaired. Look out for a new program version in the coming days!
The bug in the statistics computation is new to me. I am rather confused, as the method called is an internal Java method and should exist everywhere. I need to look into this. Could you please tell me, which Ubuntu version and which Java version you are using?

This version of FCSalyzer is still an "alpha" with many bugs. I am currently testing the program and am gradually removing the bugs. Thanks for reporting your bugs, it is highly appreciated.

Thanks,
Sven

[Anonymous]

Interesting! It's July 2021 and I have the same problem with the histogram. I gate a population of cells in a dotplot and when I want to do the histogram of just that population, the histogram plots the whole data set. Is this a bug or that I'm doing something wrong???
Thanks,
JJ

[Sven Mostböck]

Hi JJ,

please see my other response: make sure to generate a proper gate using a boolean gating strategy. here is a tutorial: https://youtu.be/RWIh2mgQCcM

Regards, Sven

[Anonymous]

Thank you very much Sven. I'll check it!
Best regards,
JJ

[Anonymous]

Hej Sven,

I am glad if I can help out. I tried different things with the statistics, since I saw that it is a problem in the java library. I use Ubuntu 14.04 LTS and intially used openJDK1.7, but installed oracle Java 1.7 addtionally. I also switched to Windows and checked if it works there, but nope...
Maybe I'm using it not correctly? I simply click on a plot and then use the statistics option under the plot menu. After selecting what I want, I hit the OK button and expect something to happen, which isn't.

Thanks for your fast response.
Jan

[Sven Mostböck]

Hm, I can't reproduce this. I can make statistics quite well with the version that is currently here on sourceforge. Could you send me an example file? I'd appreciate one (small) FCS file and the FCX document that shows the exact plot that you want to calculate statistics on. You can add them as attachement to your posts here in the forum.

Thanks,
Sven

[Anonymous]

Ok i tried once more and it does not work. Files are attached, let me know if I can help. I am not that good in java but I find it strange that there is an 'V' in the end of the first line of the Error message. Is it supposed to be there?

[Sven Mostböck]

Hi Jan, thanks for the files. It's weird, I can create the stats without error, see attached file. I am currently on Java 1.8, but the .jar is compiled to run even with 1.2.

But: I just realized something: this might have already been solved in the new version I am currently finishing. I've already replaced that particular sort-method with another one to increase speed of the stats calculation. So why don't we wait a couple of days until I uploaded the new version and test this problem again. That is probably the easiest way.

Your file was also helpful in another way - I found a bug when loading documents from different computers ;)

Thanks again,
Sven

[Anonymous]

Hej Sven,
Mh... strange enough. But anyway, Thanks for your help, and I'm looking forward for the new version. I wil let you know if I encounter other problems while using the program, so hurry up ;-).

[Sven Mostböck]

I just uploaded the new version. This is only a bugfix release - and not many bugs as is. But let's hope that the statistics calculation now works for you.

Best,
Sven

[Anonymous]

Hej Sven,
I was sick and lying in bed, so sorry for the late response. Just tested the new version and everything works fine now. Thanks alot. Even the statistics work for some odd reason. But anyway, I am happy that I can work with that now, thanks again. I will let you know if I find anything else which needs a fix ;-).

Best,
Jan