I know this question may seem strange.
I'm using Spearman correlation between gene expression profiles for various reasons (I won't go into details here). As a result, I often compare RNA-Seq and Microarray samples. For preliminary analysis, I usually grab what version of the data is easily accessible (RPKM, FPKM,...), but I'd like to dig a bit more.
Intuitively, I'd think a value similar to RPKM or such would make more sense than raw counts, which is why I usually convert raw counts to RPKM (I know they're considered obsolete for statistical analysis of the data, what I'm doing relies on the correlation)
So I ask what RNA-Seq gene expression value would be closest to a microarray equivalent ?
i.e. What would (theoretically) maximize correlation between gene expression of the same sample profiled with RNA-seq and microarray. RPKM ? FPKM ? TPM ? etc.