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YosefLab / ImpulseDE2

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Results table: although significant both is.Transient and is.Monotonous = FALSE #5

Open PsoAE opened 5 years ago

PsoAE commented 5 years ago

Hi, I do not understand the ImpulseDE2 result table. If I perform the analysis with boolIdentifyTransients = TRUE, I get some genes where is.transient=TRUE and some more genes where is.monotonous=TRUE, but some genes with padj <<0.05 have FALSE in both fields. I thought the algorithm tests tree possibilities: monotonous, transient and constant. However, according to the result table some genes are none of those three possibilities. How should I interpret those genes? Are they false positives with small p-values, but without successful fit of a transient or monotonous course? Thank you in advance.

davidsebfischer commented 5 years ago

Hi @PsoAE, I am very sorry for the late reply. The corresponding exact code is here: https://github.com/YosefLab/ImpulseDE2/blob/12197fe75946b19293ac0addee34952e211721ef/R/srcImpulseDE2_runDEAnalysis.R#L307 Essentially, the test of a sigmoid against a constant model also plays into the definition of a monotonous gene, this could result in both being False. You can definitley also come up with different classifiers, we found these ones to be stable so we are using this by default. You can copy code from the above line and adjust the classification manually on the output table!