Hi everyone,

I have a wildtype and 2 mutant samples. I have already run lrt (likelihood ratio test) and obtained > 40,000 transcripts but did not get any fold change in the output. After googling, I found that wald test (wt) would be a suitable option. Is it possible to run wald and lrt parrallely or in a comparative manner? What things I should keep in mind while filtering the results from both? How should I proceed further to find out the differentially expressed genes in mutant samples vs. wild?

Thank you!
Hello there,

If you are doing a simple comparison between wild-type and mutant samples, then you can technically do the wald test. However, in our preprint [1], all of the analyses are done with the likelihood ratio test. This is because we found that the FDR is much more believable under the likelihood ratio test then the Wald test. My general impression is that the Wald test gives too many false positives, although, the rankings are fairly comparable between the two tests.

All that being said, I would suggest simply sticking with the likelihood ratio test.

You do not get any fold change in the output because the test is inherently different. However, you can manually compute the log fold change between the samples because you have a fairly simple design. Let me know if you have any questions about doing this. The function `kallisto_table` should give you a data frame that is easily manipulated with standard tools such as dplyr.

[1] http://biorxiv.org/content/early/2016/06/10/058164.abstract