hunter-moseley
commented
2 years ago Robert,
Yes, the chi-squared test shows an association between high SD and HPD sites. I bet if you quantified the width of HPD sites against SD, you will see the wide HPD sites have high SD. If this is the case, then this description would be more informative.
Warm regards, Hunter
On Thu, Mar 17, 2022 at 3:53 PM Robert M Flight @.***> wrote:
I created a modified version of the high-peak-density detector that works in frequency space, and converted the xcalibur peak lists to frequency space.
Then I can find our own peaks that would have been part of HPD sites using the ranges from the HPD detector.
I also have the peaks that we decided had unusually high standard deviations (HighSD) from the underlying frequency level peaks.
It is trivial to find the peaks that are either HPD or HighSD, and generate a contingency table of them.
HPDHighSD FALSE TRUE FALSE 0 29 TRUE 58 49
Of course, with a contingency table, we can easily do a Chi-square test. In this case, we get a really significant p-value:
Pearson's Chi-squared test with Yates' continuity correction data: cont_table X-squared = 25.237, df = 1, p-value = 5.069e-07
@hunter-moseley https://github.com/hunter-moseley, does this make sense as a way to evaluate the overlap of the HighSD and HPD? We can plot them as well obviously.
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rmflight
I created a modified version of the high-peak-density detector that works in frequency space, and converted the xcalibur peak lists to frequency space.
Then I can find our own peaks that would have been part of HPD sites using the ranges from the HPD detector.
I also have the peaks that we decided had unusually high standard deviations (HighSD) from the underlying frequency level peaks.
It is trivial to find the peaks that are either HPD or HighSD, and generate a contingency table of them.
Of course, with a contingency table, we can easily do a Chi-square test. In this case, we get a really significant p-value:
@hunter-moseley, does this make sense as a way to evaluate the overlap of the HighSD and HPD? We can plot them as well obviously.