Methods for visualizing TPM of gene samples

Question

[Muny]

Hello everyone,

I am relatively new at analyzing RNA_seq data. I am using R studio and have a .tsv file which contains a dataframe of rna tissue samples along with their TPM values. I have noticed that most work flows begin with a raw counts file. What would be the best method or approach for analysis if all I have are tpm values?

[jared.andrews07]

For what sort of analysis? Just visualizing TPMs in a sample? Differential expression? DE from TPMs is not recommended, and while it's possible to hack something together with limma-voom, it's a much better use of your time to try to get the raw counts if differential expression analysis is your end goal.

[Muny]

I am analyzing an hpa_rna_tissue file that only includes TPM values of genes by sample. As a somewhat newbie to the space I was interested in what kind of useful information could be extracted or visualized using only the TPM values provided.

Answer 1

[swbarnes2]

If all you want is pretty pictures, learn how to use the ggplot2 library to make visualizations; it okay to use TPM for pictures. If you intend to do some real math, you need raw counts.

[Muny]

Thank you for your feedback