How to extract gene_counts_length_scaled matrix from either raw count matrix or SE object

Question

[Aditya]

Hi All, I would like to obtain gene_counts_length_scaled matrix from either raw counts or SE object. To be specific, I would like to obtain length scaled matrix from GTEX (only raw counts or SE object from recount3 can be downloaded for gtex datasets). Later on, I would need to compare gene expression across species for which I think length scaled counts can be an input for DGE analysis so that gene lengths are not a contributing factor. Please let me know how can I perform this analysis in R.

The other option is to download the raw counts from the two species, merge them, and use them for DGE.

Thank you, Aditya

Answer 1

[ATpoint]

If SE is a SummarizedExperiment and gene_counts_length_scaled is a element of assayNames(SE) then it is assay(SE, "gene_counts_length_scaled") to access the data.

The other option is to download the raw counts from the two species, merge them, and use them for DGE.

A general note: Be sure that data you want to quantitatively compare has been generated in the same lab, same kit, batch, day, everything. If not much of what you will be picking up is batch effects, so any technical differences that overshadow true biological signal. If that is news to you I recommend diving into the basics of experimental design and RNA-seq analysis. In general, one can never compare independent datasets pretending they were produced in the same experiment.

Also, you might want to read up on what gene_counts_length_scaled actually is, because common DE tools assume that length information has not been cancelled out as the model needs the full count information to be informative.