I want to use ImpulseDE2 software to identify genes that are differentially expressed over time (I have samples from 12 patients at 4 time points). I have two questions and unfortunately trying to contact the developers failed.
1) Does somebody know whether ImpulseDE2 can deal with missing data? For some patients one timepoint is missing. There is no error message when I run the software, but I am concerned whether ImpulseDE2 can deal with this. For me it is not obvious from the published benchmark article (https://www.ncbi.nlm.nih.gov/pubmed/30102402).
2) 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?
I appreciate every tip. Thanks in advance!