Question: how I can prepare data for heat-map?
gravatar for mirzahosseini.z
2.4 years ago by
mirzahosseini.z0 wrote:

I want to show my proteomics data (protein abundance) by heat-map. I have 1 control and 4 treatment conditions. But I don't know how exactly I can prepare data for heatmap. Actualy, I've calculated fold changes for each sample by dividing protein abundance of that sample to protein abundance of correlated control. Then I calculated log 2 for fold changes. Is it the right way to calculate fold change? If yes, the heatmap shouldn't have control, and it will be just for representing treatments. Right? After clustering I don't know how I can interpret it. Is it enough to represent just similarity by clustering? Or I am expected to eliminate or change some of my data according to the result of clustering?

Thanks in advance Zahra

rna-seq • 1.4k views
ADD COMMENTlink modified 2.4 years ago by Devon Ryan96k • written 2.4 years ago by mirzahosseini.z0
gravatar for Devon Ryan
2.4 years ago by
Devon Ryan96k
Freiburg, Germany
Devon Ryan96k wrote:

Normally one plots either the intensity values or some variant of log-transformed intensity values. Don't make a heatmap of fold-changes, that's largely worthless. You don't have to do any clustering at all. If you'd like to, then you might see how your treatment replicates cluster and see if you have any proteins that co-vary.

ADD COMMENTlink written 2.4 years ago by Devon Ryan96k
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