Hi there
Can anyone explain to me how to use the ESTIMATE package in RNA-seq analysis? 
I want to calculate immune scores and stromal scores by employing the ESTIMATE algorithm, then analyze the relationship of immune/stromal scores with subtype classification and cytogenetic risk by one-way analysis of variance, but I don't know how to do this!

I will be grateful for any help you can provide.
A vignette PDF comes installed with the package, and should be located at:

 - R/x86_64-pc-linux-gnu-library/4.0/estimate/doc/ESTIMATE_Vignette.pdf

In this vignette, they use some data that comes bundled with the package (*R/x86_64-pc-linux-gnu-library/4.0/estimate/extdata/sample_input.txt*), which represents Affymetrix U133 microarray data that appears to be normalised and transformed by log [base 2].

So, if you have RNA-seq data, I would normalise the data in the usual way, and then transform via rlog or vst. Then, with ESTIMATE, use the rlog or vst expression levels.

Kevin