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closehow to interprete Prevalence
Posted by OwenQin on 31 Oct 2013 at 01:56 GMT
dear Dr. Elhanan Borenstein & other authors,
The first time I saw"prevalence" in the paper I interpreted it as 'proportion'. For a given gene, the prevalence of it is the proportion of it to a given genome. Assuming that the length of a genome is L and the length of gene is l, so the proportion is l/L. (assuming the gene as a single copy gene.)
But it seems that 'prevalence' and 'proportion' are not the same concept. Where am I wrong? Thanks.
RE: how to interprete Prevalence
Rogan replied to OwenQin on 31 Oct 2013 at 23:40 GMT
Hi Owen,
Thanks for your interest in our method. The "prevelance" of a gene j in genome k, e_kj in Eq 3, is a generic way to denote the amount of the gene in the genome. In practice, this is usually expressed as the total nucleotide length for the gene (summed over all copies of the gene in the genome, if applicable), or the number of copies of the gene (the total length / the typical length of the gene). Whether Eq 3 is given in terms of the nucleotide length or copies depends on whether the abundance of genomic elements E_ij is specified in the number of reads or in the number of copies (respectively).
I hope that answers your questions.
Best,
Rogan