This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Data format to produces a heatmap like this

Hi,

My question is simple. I am just not just that how to arrange my data matrix to produces a heatmap to show a disticnt band in each tissue (preferential expression) like Figure 4 of this article.

Thanks

rna-seq r heatmap
• 3,676 views • link
updated by Ram Ram • written by prp291 prp291

1 answer

Try to play with different clustering algorithms (i.e ward, ...) and different scales and scale colors when drawing your heatmap. In their methods they say that they used heatmap.2 (R package).

Hint: by limiting the scale, you avoid outliers from messing up with your scale and heatmap colors.

• 0 views • link
updated by Ram Ram • written by Alternative Alternative

I tried different clustering algorithm but none of them seems to work for me. Thanks though

• 0 views • link
written by prp291 prp291

Do you know that you have such a structure for your data ? If you know which tissue each row corresponds to, you can just reorder your matrix to group the rows by tissue. If there is a structure corresponding to tissues, it should become apparent (possibly with the proper scaling as Pierre suggested).

• 0 views • link
written by Jean-Karim Heriche Jean-Karim Heriche

Log in to answer this question.

More posts like this