I hope this message finds you well. I am writing to express my sincere appreciation for the incredibly useful tool you've developed. I have been utilizing it to generate APA plots, and I must say, the functionality is quite impressive.
However, I have encountered an issue while working on generating APA plots. I am using the following code:
fanc aggregate /path/to/hic_10kb.hic /path/to/loops.bedpe output.agg -p output.pdf --loop-strength loop_strength.txt --loops -e -l --rescale -v center -i 1 --vmin 0 --vmax 2
The APA plots generated appear to show significant differences, but when I attempt to create boxplots and perform significance analysis using the --loop-strength generated files across four groups, there is a complete lack of variation. I am puzzled as to why this might be the case.
Could you please shed some light on how the loop strength is calculated? I am curious to understand the discrepancy between the visual inspection of the APA plots and the statistical analysis results from the loop strength data.
Thank you very much for your time and assistance. I look forward to your guidance on this matter.
nieyage
commented
1 week ago
I hope this message finds you well. I am writing to express my sincere appreciation for the incredibly useful tool you've developed. I have been utilizing it to generate APA plots, and I must say, the functionality is quite impressive.
However, I have encountered an issue while working on generating APA plots. I am using the following code:
fanc aggregate /path/to/hic_10kb.hic /path/to/loops.bedpe output.agg -p output.pdf --loop-strength loop_strength.txt --loops -e -l --rescale -v center -i 1 --vmin 0 --vmax 2The APA plots generated appear to show significant differences, but when I attempt to create boxplots and perform significance analysis using the --loop-strength generated files across four groups, there is a complete lack of variation. I am puzzled as to why this might be the case.
Could you please shed some light on how the loop strength is calculated? I am curious to understand the discrepancy between the visual inspection of the APA plots and the statistical analysis results from the loop strength data.
Thank you very much for your time and assistance. I look forward to your guidance on this matter.