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Experiment File - All Genes or Only Significant Genes?

Hello,

For the experimental data file, is it best to upload data for all genes or to pre-filter based on significant changes and derived values? I saw an earlier post saying to upload data for all genes, but when I do that, some pathways become impossible to read because there are so many data points being displayed. The built-in filtering only greys out data instead of removing it, so my pathway remains clogged with grey or white data points that I'm not interested in.

Is it okay to pre-filter data if I'm just trying to display it on a pathway?

Any help would be greatly appreciated,
Charles

RE: Experiment File - All Genes or Only Significant Genes?
Answer
7/10/18 9:10 AM as a reply to Charles Hem.
Dear Charles

anyway this is up to you, however if you don't filter the same spot is the same geen accross experiments.
Only if you perform an enrichment test (pageman) than you must not filter, as it uses the active experiment set as the background.
Are you using wheat or any other polypoloid genome? Usually the mpas are made to fit a "typical" diplod. You can of course also change the size of each spot.

HtH

Bjrön

RE: Experiment File - All Genes or Only Significant Genes?
Answer
7/10/18 3:24 PM as a reply to Björn Usadel.
Hi Bjorn,

That answers my question, thank you very much! I'm working with Brachypodium distachyon. It fit fine in most pathways except for the full Overview pathway that displays every single bin, so that's okay.

Thank you!
Charles