ppavlidis
commented
6 months ago We should change the focus of this issue to be just for the API - the GUI does not need changes IMO especially as described. I agree having a switch like this in the API could be useful, though it's not hard for users to do this filtering.
About the UI, non-specific probes are viewable on the elements tab (sort by 'hits' to enrich for them; hits refers to number of genome alignments, and elements with too many alignments are not assigned genes at all; current threshold is 10, I believe)
Also, on each microarray platform page you can see the mapping statistics
Now, we don't have a line there for "number of non-specific probes", so we could add that, but that's high-level information.
In the REST API, we have a switch to include nonspecific probes when selecting expression data or differential expression results per gene. This is necessary because we don't want to show probes that map to other genes.
To make it clear to users which probes are affected by this, I think we should either include a list in the platform page.
In the REST API, we could add an option to list non-specific probes or exclude them.