relative abundace?

[plant272]

Hello Arkadiy,

--norm, if include this flag, the gene counts for each iron gene category to be normalized to the number of predicted ORFs in each genome or metagenome. Without normalization, FeGenie will create a heatmap-compatible CSV output with raw gene counts. With normalization, FeGenie will create a heatmap-compatible with 'normalized gene abundances'.

I compared the normalization and non-normalization data and found the normalized gene abundances if include this flag is 1000 times bigger than the percentage of “raw gene counts/predicted ORFs numbers” I calculated by myself. Is that correct? Thank you.

[Arkadiy-Garber]

Hi,

Thanks for your interest in FeGenie! Yes, that is correct. By default, FeGenie will "inflate" the normalized numbers by 1000 (so to that you don't have to stare at tiny numbers (e.g. [0.001, 0.023] vs [1, 23], the latter is easier to compare by eye). You can set -inflation 100, and it will multiply the "raw gene counts/predicted ORFs numbers" by 100 - at which point, you will be dealing with percentages. You can also set -inflation 1, and it will report the raw quotient of "raw gene counts/predicted ORFs numbers". Does this make sense? Let me now if you have any other questions.

Thanks!
Arkadiy