Heatmap for protein abundance.

Question

[Vivian Den]

Hi, I have a proteomics data, which has been analyzed using Proteome Decoverer 2.4. The data has protein accession number ,abundance. I wonder how I perform a heatmap for protein abundance with clustering? Thank you for your help!

Update:If I have three control and three treatment samples tested in expression in some genes. To perform the heatmap, should I firstly received the fold changes? How I calcute these values?

Answer 1

[GenoMax]

See if this tutorial by @Kevin Blighe is of help: https://github.com/kevinblighe/E-MTAB-6141

[Vivian Den]

Hi genomax, thank you for your reply! I have updated my post with one more question on fold changes.

[Kevin Blighe]

The heatmap is usually generated on the transformed expression values (usually logged values and / or Z-scaled). You can also plot the heatmap using the log [base2] fold-changes, if you so desire.