How To Clustering Data Based On Reference?

Question

[quge856]

Dear All,

Give a data set (RNA-seq -> RPKM value -> standardisation), one of them (let me say gene X1) is my interest, I want to figure out how many other genes expressed under the similar expression pattern as X1, in other words, how to clustering data based on a reference gene?

I've tried hard clustering (k-mean) and also soft clustering way (fuzzy), none of them could work out, :(

Best,

Answer 1

[Istvan Albert]

You are thinking about this the wrong way. You don't cluster for a target, you cluster then identify similar groups.

So in your case cluster the data then look for the cluster that contains the gene of interest.

[quge856]

for sure, it's a wrong way to detect genes under similar expression pattern via clustering, maybe there are other methods could do that. Thank you anyway!