Interpretation of log2 fold changes in the result

[Kyung-TaeLee]

Hi, thank you for providing such a great tools.

I am currently analzying UTR length shift using the function "DetectUTRLengthShift". Among the parameters of DetectUTRLengthShift function, you can specify population.1 and population.2. Can you tell me how they correpond to numerator and denominator in terms of log2 fold changes in the output?. I examined the source codes of DUtest and the function implement DEXseq function for the differential test. There was no code block that specify how the contrast will be performed so in the default setting, log2 fold changes will be log2 (population.2 expression/ population.1 expression). However, the manual seems to be telling that population.1 will be the numerator and population.2 will be the denominator. Which senario is true?

Best regards,
Kyung-Tae Lee

[rj-patrick]

Hi @Kyung-TaeLee,

The reported log2 fold changes use population.1 as the numerator and population.2 as the denominator.

Cheers,
Ralph