Hi everyone,
I am new to R and have been tasked with analyzing a dataset that only provides FPKM (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE223176). I know that FPKM is not meaningful for sample-wise comparison but it seems they only give the FPKM data.
I have been reading threads regarding this topic but could not figure out a detailed pipeline and input code that I need to use to solve the task. All that I know is it is better to transform the data to log2(FPKM+0.1) and apply limma-trend. However, when I try to follow the user guide of Limma, it seems they only use the integral-number-count-table.
Could someone help me by providing a source that I can read or some example code? I truly appreciate any help since I have no clue what should I do now...
Agree with ATpoint
Salmon is really easy to run, you can even run it on your laptop if you aren't familiar with using a computer cluster. You can download a recent binary (v1.10) here:
https://github.com/COMBINE-lab/salmon/releases/tag/v1.10.0
After decompressing, you can directly execute the Salmon program on Linux or Mac.
It's worth learning these basic steps to process RNA-seq data.
Thank you so much for your answer. I will try to do as your suggestion.