i have a specific need to cluster more than 1K genes based on their expression profile. I want to extract then just the genes in clusters with the same expression profile. My first attempt was to set the optimal K with gapstat and using kmeans to mark my expression atlas with the cluster identifier and then extract the genes from a specific cluster by subsetting the dataframe. This didnt work because kmeans tries to put together genes even with different expression profile.
So do you have any suggestion to accomplish this?
- i want to cluster a big expression atlas
- extract the gene IDs with similar expression profile
thanks in advance
i saw this post https://support.bioconductor.org/p/93424/ about pheatmap which would be ideal but i cannot figure out how to check the clusters identifier in order to use cutree function