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...