impulseDE2 input
Entering edit mode
4 months ago

Hello everyone

I am using impulseDE2 for the longitudinal analysis. I found this link which indicates not to use normalized count and decided to use raw count data for the analysis. I also found computeSizeFactors ( function within the impulseDE2 which means by default it will calculate sizefactor for normalization.

But I have seen many post where they mention to use normalized count from DESeq2. I am bit confused about the "input" file for impulseDE2.

I would appreciate all the suggestions.

normalized count input raw impulseDE2 • 224 views
Entering edit mode
4 months ago
kelen ▴ 180

If I am not mistaken impulseDE2 does indeed require raw counts as it does it's own DE, including using DESeq2 for some steps:

"ImpulseDE2 is based on a negative binomial noise model with dispersion trend smoothing by DESeq2 and uses the impulse model to constrain the mean expression trajectory of each gene" - from here

The results of significantly DE genes were roughly the same as they were with DESeq2 LRT, when I tried it a while ago, but I didn't fully understand everything it was doing so I opted not to use it.


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