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Differentiate DTU from DGE? #48

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fruce-ki opened this issue Mar 1, 2018 · 0 comments
Closed

Differentiate DTU from DGE? #48

fruce-ki opened this issue Mar 1, 2018 · 0 comments
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enhancement Suggestions for better performance or better presentation.
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0.6.3

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fruce-ki commented Mar 1, 2018 •
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Often, high-ranking DTU hits are just gene switch on/off events, where the very few transcripts seen in one of the two conditions can create an artificially massive change in isoform proportions.

Set better noise criteria, or find a way to flag and discount gene on/off events and marginal above-noise cases.
It is not RATs' intention to identify significant DGE in general, but when one of the conditions is very lowly expressed, it leads to results I do not find particularly convincing.
@fruce-ki fruce-ki added this to the 0.7.0 milestone Mar 1, 2018
@fruce-ki fruce-ki added the enhancement Suggestions for better performance or better presentation. label Mar 1, 2018
@fruce-ki fruce-ki self-assigned this Mar 1, 2018
@fruce-ki fruce-ki modified the milestones: 0.7.0, 0.6.3 Mar 8, 2018
fruce-ki added a commit that referenced this issue Mar 8, 2018
@fruce-ki
fixes #51 and closes #48
d425a95 
- 51: fixed the bug where accidentally the same isoform must exceed
noise in both conditions.
- 48: The noise threshold is applied to the total gene abundance as
well, preventing genes that are switched off in one condition from
creating wild proportions and exaggerated effect sizes.
@fruce-ki fruce-ki closed this as completed Mar 8, 2018
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