Question: Heatmap for protein abundance.
0
gravatar for Vivian Den
4 weeks ago by
Vivian Den0
Vivian Den0 wrote:

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?

heatmap; proteomics • 120 views
ADD COMMENTlink modified 4 weeks ago • written 4 weeks ago by Vivian Den0
1
gravatar for genomax
4 weeks ago by
genomax91k
United States
genomax91k wrote:

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

ADD COMMENTlink written 4 weeks ago by genomax91k

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

ADD REPLYlink written 4 weeks ago by Vivian Den0

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.

ADD REPLYlink written 4 weeks ago by Kevin Blighe66k
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