How to create the matrix of expression values from different gene lists for generating heat map?

Question

[mirza]

Hi,

I have several lists of up-regulated and down-regulated genes (with their fold change values). Different genes are expressed in different conditions. Now how to create the matrix for heat map generation using all these genes lists? As I have hundreds of genes, manually searching each gene in all the lists and feeding its respective fold chane will be insane

[Carlo Yague]

This seems like a very basic task... Can u script with R or python ? or do you want an answer based on Excel ?

[mirza]

better be excel right now. I am trying to learn R

[Jean-Karim Heriche]

https://nsaunders.wordpress.com/2016/08/25/data-corruption-using-excel-12-years-and-counting/

[mirza]

I get it, its really a bad choice to use excel. Please suggest some solutions. Please direct me to some tutorials or web page or forum discussions where I can find the answers.

[mirza]

Please suggest some solution with R, I can us it to some extent. I know we can use ggplots but I think I need to create the matrix first?

[Jean-Karim Heriche]

Yes you need a matrix first. There are plenty of R tutorials around. Here is one on loading data into R. For data wrangling, you have the choice of several packages such as dplyr (tutorial) or data.tables (introduction to data.tables).

Answer 1

[Carlo Yague]

With excel, you can create a column with all the gene IDs you are interested in, then use Vlookup to search the expression value corresponding to the IDs in the different tables (conditions).

In R, you can use merge() to merge dataframes based on the geneID column or whatever.