I have RNAseq data (gene count, FPKM, and TPM values) from RSEM and would like to cluster it and produce a heatmap using the R package pheatmap. I would like to perform a hierarchical clustering analysis to ensure that samples are clustering together in a logical way (i.e. controls are clustering together and treated clustering with treated). I would like to do this using TPM values from each of the samples to see a heatmap of TPM values clustered by sample. Ideally, I am trying to verify that the control samples are correlated and the treated samples are correlated.
I am a novice when it comes to bioinformatics and using R and have spent an embarrassing amount of time pouring over pheatmap manual and internet tutorials on how to do this.
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So, what is the actual question? What doesn't work?
Please also post your code, people will be more eager to point out your mistake.