Relative RNA abundance in Metatranscriptomes: how to normalize RNA abundance by DNA
Hi All, I have calculated DNA and RNA abundance following the method described in this paper: https://www.nature.com/articles/nature13568
my question now is: is there a way that I normalize the RNA levels (from the metatranscriptome) using my abundance over the metagenome for the same sample? what is the best practice?
I'm thinking you need to divide the transcriptome levels by the genome abundances for those species. Any advice would be highly appreciated. Thanks.
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If your goal is differential expression analysis, you could just include the abundance over the metagenome as a covariate in your design formula. In this way, the statistical inferences will be adjusted for this value.
thanks for your response. I was hoping to adjust the abundance of transcriptome levels by the metagenome levels. Like for instance if I have RNA levels for some gene from species A as 100 units, and then RNA levels from another gene from species B as 200 units, but the DNA levels for species B is also twice as much as that for species A, hence if we account for the metagenome levels than more or less the expression levels for these two genes should be the same. Is there a way that we could incorporate these two? Thanks
I still think to include it as a covariate in your downstream statistical models, or is there are particular reason why this would not be ideal?
What is the end goal? - differential expression or to literally just directly adjust the RNA levels based on DNA content?
the end goal is to do a cross species expression level comparisons within one metatranscriptome sample.