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Consequently, RAId_aPS is able to provide a calibration-free protocol for accurate significance assignment and for combining search results.
The weak pairwise correlations among different scoring functions implies that the outlined strategy above may still provide decent significance assignment.
That is, the resulting significance assignment is valid only when scoring functions considered are uncorrelated, or at most weakly correlated.
We are currently investigating the impact of the existence of these types of false positives on the statistical significance assignment.
Suppose one has obtained a list of candidate peptides from some analysis tools that provides only crude statistical significance assignment or no significance assignment at all, it is possible to upload this list of peptides along with the spectrum to RAId_aPS to get a reassignment of statistical significance via mode (iii) of RAId_aPS.
When using search methods that do not have a theoretical model for the score distribution or when the quality of the score model [11] is poor, one may wish to use a more conservative statistical significance assignment.
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This may help in preventing exaggerated/inappropriate statistical significance assignments.
This paper mainly focuses on the data analysis, especially providing accurate statistical significance assignments for peptide candidates in peptide identifications.
As a consequence, SaddleSum enables researchers to place confidence in its significance assignments to small terms that are often biologically most specific.
Darker colors represent nodes that are assigned with statistical significance, while lighter colors represent non-significant assignments.
The most significant functional assignments are shown in Table 1, along with the p-value for the significance of each assignment and the total number of smoking correlated genes within each category.
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