Hello! I’m a bioinformatician processing a peak table of metabolomic data and I’m interested in a functional analysis of the peak table. However, as a sanity check, I tried to see if different filtering cut-offs during the “Data Filtering” phase would change my results in any way. I noticed that regardless of which value I entered in the “percentage to filter” slider (I tried 0, 20, 40, and 99%) the results were entirely the same. All other parameters were constant (mummichog @ p-value = .05, autoscaling and quantile normalization).
I tried this with different datasets and had the same issue. Naturally, the results did change between different datasets, but not after adjusting the filtering percentage.
Next, I tried to explore the issue in MetaboAnalystR following the functional analysis tutorial. I attempted to use the FilterVariable() function to use IQR filtering at 40%. I got an “unused argument” error when using the filter.cutoff argument (which appears as a possible argument using “?FilterVariable”, see here: FilterVariable: Methods for non-specific filtering of variables in xia-lab/MetaboAnalystR: An R Package for Comprehensive Analysis of Metabolomics Data), and upon investigating the source code for FilterVariable(), I noticed there is no filter.cutoff argument in the definition of the function. This would appear to me to be the source of this issue. I don’t see how to to pass a percentage to filter out to the function, and it isn’t clear to me from the source code of the function what it is doing by default.
If there’s something I’m missing please let me know but otherwise I wanted to report that there currently appears to be no way to adjust data filtering for peak table functional analysis. I’m using MetaboAnalystR version 4.0.0