Hi,

I created a RangedSummarizedExperiment object via the create_rse() function of the recount3 package (project == "LIHC" & file_source == "tcga"). The next step would be to extract the read counts for all available genes to use these counts for normalization and transformation via the estimateSizeFactors and vst function of DESeq2.

If I understand it correctly after using create_rse() I only have raw base-pair coverage counts stored in the "raw_counts" assay, which is not what I need.

In the quick start guide is written:

Using transform_counts() you can scale the counts and assign them to the “counts” assays slot to use them in downstream packages such as DESeq2 and limma.

So it looks like that transform_counts() is the function which gives me the gene read counts I need for my further analyses. But what about the compute_read_counts() function? What is the difference between transform_counts() and compute_read_counts()?

Thanks in advance.

Mario

Hi,

Thank you for using recount3.

compute_read_counts() http://research.libd.org/recount3/reference/compute_read_counts.html gives you actual read counts similar to other RNA-seq processing pipelines you might be familiar with. transform_counts() http://research.libd.org/recount3/reference/transform_counts.html gives you scaled counts such that counts are based on a total library size of 40 million mapped reads (by default). You likely just need compute_read_counts() for your use case.

compute_read_counts() is equivalent to recount::read_counts() http://leekgroup.github.io/recount/reference/read_counts.html whereas transform_counts() is similar to recount::scale_counts() http://leekgroup.github.io/recount/reference/scale_counts.html. See this older related thread recount counts in the example experiment.

Best, Leo