Proteomics Data Visualisation in Heat Maps

Question

[ahmedakhokhar]

Apologies for such a basic question; I am new to proteomics data visualisation and want to make heat map of mass spec proteomics qualitative data. I have the data into two columns as follow:

log2 fold change protein IDs

9,83 P15992

7,10 P39004

6,65 P06738

6,11 P40043

6,11 P32775

6,06 Q04432

So far I read and follow different published material as in publication (Melissa Key BMC Bioinf.2012 )(http://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-13-S16-S10).

Problem: Most of the times people working with the proteomics data have more columns (conditions), and that is a bit confusing for new comer like me who has data from only one condition,

Question: is there any software or R/python code to start with in displaying the above-mentioned data.

Thanks ! good day

Answer 1

[Benn]

See previous post on stackoverflow:

http://stackoverflow.com/questions/15749132/r-heat-map-with-only-one-column

[ahmedakhokhar]

Thanks, how would you explain the coloring and color differences in image() and interpret the result since there is no clustering ?

[Benn]

If you have only one column, you can sort instead of clustering.

The colors in a "heatmap" should tell you something about the intensity of your values, I am not sure if that's what you're asking?