Hi everyone.
First of all, thank you so much for the ReCount3 project as it helps a lot on analysing the public datasets. As shown from the title, being a "newbie" on bioinformatics/coding, i have a hard time to get TPM values from the data download via ReCount3.
Basically i tried to follow the manual (https://bioconductor.org/packages/release/bioc/manuals/recount3/man/recount3.pdf) but still i have no idea on the follow-up.
My question is: How do i able to get the TPM value for genes after the step of: recount::getTPM("RangedSummarizedExperiment_of_datasetx), because i do not want to do DEseq2 but just to get a dataframe with TPM value for gene (row) in different samples (column)
## Once you have your RSE object, you can transform the raw coverage
## base-pair coverage counts using transform_counts().
## For RPKM, TPM or read outputs, check the details in transform_counts().
assay(rse_gene_SRP009615, "counts") <- transform_counts(rse_gene_SRP009615)
## Compute TPMs
assays(rse_gene_SRP009615)$TPM <- recount::getTPM(rse_gene_SRP009615)
colSums(assay(rse_gene_SRP009615, "TPM")) / 1e6 ## Should all be equal to 1
Because since they are "all equal to 1 now" from the manual, i really do not know what to do. I tried to do: assay(rse_gene_SRP009615,"TPM") but it does not work.
Thank you so much for the help.
(Sidenote: i hope the GTEx dataset for the brain tissue in ReCount3 can be further broken down into sub-section in the brain like in GTEx portal so that i can get specific part of the brain like frontal cortex.)
Regards, David
Thank you very much for the detail explanation and teaching. That's very helpful!