Interesting thought. I am not familiar with these analyses, but it would not
surprise me if your intuition is correct.
J
> On Sep 19, 2021, at 1:00 PM, Ferenc Tibor Kagan wrote:
>
> Dear r-sig-phylo community
>
> I am writing to you in hopes of you giving me your inputs on a specific topic.
>
> I noticed a rise of use of PCMs when it comes to gene expression data lately.
> Many of these studies before fitting a specific model to their expression
> data do several normalization steps. The common steps in order are to
> normalize for sequencing depth and gene length, normalize in between
> replicates within species and finally to normalize across species. For within
> species and across species I have seen TMM normalization method being used
> (from edgeR package) or batch effect removal (f.ex. Combat-seq function from
> sva package).
>
> My concern is the final normalization step, namely to normalize continuous
> data across species before model fitting. By doing so wouldn't one minimize
> the phylogenetic signal present in the dataset, therefore affecting the best
> fitting model?
>
> Thank you in advance for your answer.
>
> Best regards,
> Ferenc Kagan
>
> [[alternative HTML version deleted]]
>
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