Hi Sven,
I am really happy with your software. On Windows it runs perfectly for me. But at Ubuntu 12.04 I am not able to do statistics for histograms, especially if I am having an overlay of 2 files or more than 1 marker in the histogram. Then statistics does not work. Do have any suggestions/recommondations for me to fix that? Is it maybe due to an old Java version (sorry I do not know the java version on the Linux PCs). I also have to add that I am really not familiar with all this computer-software-facts... sorry for that :)
Thank you so much for your efforts,
Greetings,
Katrin
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thanks for your bug report. I do not have a solution for you problem at the moment. I need to test the program on Ubuntu myself first. On Linux, the Java version is often "OpenJDK" in difference to "Oracle Java" on Windows. That might be the reason for the problem.
Two questions:
1) which version of FCSalyzer do you use?
2) can you do statistics of regular dot plots (for example quadrant statistics)?
I will take a look into it. Unfortunately that might take some time.
Best regards,
Sven
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Hi Sven, thanks for your fast reply!
I use the 0.9.8-alpha version of FCSalyzer.
On a normal dot plot I can do statistics. For the histogram it is not that easy. I will give you an overview about my procedur:
1) I do a density plot (FSC-A and SSC-a) and gate a specific population (=G0)
2) in the G0 population i gate out the single cells in FSC-A vs FSC-H (=G1)
3) then i draw a histogram for the B3 channel and let show only the G1 population. In this histogramm a put markers for 4 different peaks. But statistics only works for the first marker I put. Afterwards the program srews up and cannot do any staitstics anymore. Also if I delete the whole histogram and draw a new one statistics do not work anymore for that.
Thank you so much for your efforts which I really appreciate!
Greetings
Katrin
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Hi Sven,
thank you for your reply! I do not know if you received my reply as I cannot see it here as aPost that's why I am sending a new one :) To your questions:
ad 1) I use FCSalyzer 0.9.8-alpha
ad 2) at dot/density plots the statistic works. Only if I add a histogram there are problems. The program will do a statistics but after adding markers statistics are not possible anymore. But here my procedure in more detail:
1) I draw a density plot (FSC-A vs SSC-A) and gate a population (=G0)
2) Within G0 I gate singel cells using FSC-A vs FSC-H (=G1)
3) Then I draw a histogram for B3-A and choose only the G1 gate. Then I add 1 marker M1 if I added statistivs before this point and was succesfull the staistic for M1 is shown. If I add now a second marker M2 into the histogram then nothing happens and I also cannot add a new statistic.
I appreciate your efforts as I am really no computer-professionalist- Sorry for that :)
Greetings
Katrin
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thanks for the reply.
The reason why you can't see your posts: This forum is moderated, which means that I have to approve posts before they become visible. That is meant to prevent spammers from writing horrible postings.
Thanks for the details on your process. I will take a look into it, but it will take some time (weeks).
best,
Sven
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Anonymous
Anonymous
-
2022-05-27
I can't see event count when two or more .fcs files re plotted together as overlay. any solution?
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Do you mean the y-axis on histograms?
It depends on the scaling of the y-axis.
Usually, histograms are scaled so that the peak channel "fills" the y-axis - this is called "Local maximum". If there is only one overlay, FCSalyzer can then print the event-count for this channel on the y-axis. However, if there are two datasets are shown as overlays, they have different event counts for the peak channel. Hence, the y-axis is empty, because there is no correct value for it.
Use "Global Maximum" or "Manual Scale" in the "Format Plot/Overlay" menu to define a scale that applies to all overlays. Then, the event counts will be shown accordingly on the y-axis.
Regards,
Sven
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Hi Sven,
I am really happy with your software. On Windows it runs perfectly for me. But at Ubuntu 12.04 I am not able to do statistics for histograms, especially if I am having an overlay of 2 files or more than 1 marker in the histogram. Then statistics does not work. Do have any suggestions/recommondations for me to fix that? Is it maybe due to an old Java version (sorry I do not know the java version on the Linux PCs). I also have to add that I am really not familiar with all this computer-software-facts... sorry for that :)
Thank you so much for your efforts,
Greetings,
Katrin
Hi Katrin,
thanks for your bug report. I do not have a solution for you problem at the moment. I need to test the program on Ubuntu myself first. On Linux, the Java version is often "OpenJDK" in difference to "Oracle Java" on Windows. That might be the reason for the problem.
Two questions:
1) which version of FCSalyzer do you use?
2) can you do statistics of regular dot plots (for example quadrant statistics)?
I will take a look into it. Unfortunately that might take some time.
Best regards,
Sven
View and moderate all "Contact the author" comments posted by this user
Mark all as spam, and block user from posting to "Discussion"
Hi Sven, thanks for your fast reply!
I use the 0.9.8-alpha version of FCSalyzer.
On a normal dot plot I can do statistics. For the histogram it is not that easy. I will give you an overview about my procedur:
1) I do a density plot (FSC-A and SSC-a) and gate a specific population (=G0)
2) in the G0 population i gate out the single cells in FSC-A vs FSC-H (=G1)
3) then i draw a histogram for the B3 channel and let show only the G1 population. In this histogramm a put markers for 4 different peaks. But statistics only works for the first marker I put. Afterwards the program srews up and cannot do any staitstics anymore. Also if I delete the whole histogram and draw a new one statistics do not work anymore for that.
Thank you so much for your efforts which I really appreciate!
Greetings
Katrin
View and moderate all "Contact the author" comments posted by this user
Mark all as spam, and block user from posting to "Discussion"
View and moderate all "Contact the author" comments posted by this user
Mark all as spam, and block user from posting to "Discussion"
Hi Sven,
thank you for your reply! I do not know if you received my reply as I cannot see it here as aPost that's why I am sending a new one :) To your questions:
ad 1) I use FCSalyzer 0.9.8-alpha
ad 2) at dot/density plots the statistic works. Only if I add a histogram there are problems. The program will do a statistics but after adding markers statistics are not possible anymore. But here my procedure in more detail:
1) I draw a density plot (FSC-A vs SSC-A) and gate a population (=G0)
2) Within G0 I gate singel cells using FSC-A vs FSC-H (=G1)
3) Then I draw a histogram for B3-A and choose only the G1 gate. Then I add 1 marker M1 if I added statistivs before this point and was succesfull the staistic for M1 is shown. If I add now a second marker M2 into the histogram then nothing happens and I also cannot add a new statistic.
I appreciate your efforts as I am really no computer-professionalist- Sorry for that :)
Greetings
Katrin
Hi Katrin,
thanks for the reply.
The reason why you can't see your posts: This forum is moderated, which means that I have to approve posts before they become visible. That is meant to prevent spammers from writing horrible postings.
Thanks for the details on your process. I will take a look into it, but it will take some time (weeks).
best,
Sven
I can't see event count when two or more .fcs files re plotted together as overlay. any solution?
Do you mean the y-axis on histograms?
It depends on the scaling of the y-axis.
Usually, histograms are scaled so that the peak channel "fills" the y-axis - this is called "Local maximum". If there is only one overlay, FCSalyzer can then print the event-count for this channel on the y-axis. However, if there are two datasets are shown as overlays, they have different event counts for the peak channel. Hence, the y-axis is empty, because there is no correct value for it.
Use "Global Maximum" or "Manual Scale" in the "Format Plot/Overlay" menu to define a scale that applies to all overlays. Then, the event counts will be shown accordingly on the y-axis.
Regards,
Sven