Hi there,
We ran into an issue while testing different parameter values in the MSpurity Galaxy tool suit (first with msPurity.averageFragSpectra but then checked and found that it is also the case for msPurity.filterFragSpectra).
We wanted to determine whether using an abundance threshold would lead to better results with our datasets, so we wanted to compare the default value of the corresponding parameter (Relative abundance threshold [--ra]) which is 0 (no filter) with a 5% threshold. Since the value in the Galaxy wrapper should be given between 0 and 1 (see bellow), we entered "0.05"
But then we saw no change in the outputs. We looked at the results, and saw that the "ra" column was in percent (see bellow) and considered values bellow 5% as not to filter (and thus it was not filtered).
We looked at the MS purity R package documentation and found no specification about units for the input value
nor for the output value
that could suggest that the two of them (input and output values) would be in the same unit (and thus in percent).
To test our hypothesis, we rerun the analysis using a threshold of 0.8 (having spotted some lines with ra values below 0.8 %), and then these spotted lines were correctly tagged as to filter.
In light of these elements, we suspect a typo in the Galaxy wrapper, that would have been set to "0 to 1" instead of "0 to 100" for this specific parameter (and same for the other tool with the same parameter).
Does anyone have experience with this parameter and/or any feedback about that? @yguitton maybe?
Mélanie