Question: How to create the matrix of expression values from different gene lists for generating heat map?
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gravatar for mirza
3.8 years ago by
mirza110
India
mirza110 wrote:

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

heat map matix gene lists • 1.9k views
ADD COMMENTlink modified 3.8 years ago by Carlo Yague5.0k • written 3.8 years ago by mirza110

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

ADD REPLYlink written 3.8 years ago by Carlo Yague5.0k

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

ADD REPLYlink written 3.8 years ago by mirza110

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

ADD REPLYlink written 3.8 years ago by Jean-Karim Heriche22k

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.

ADD REPLYlink written 3.8 years ago by mirza110

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?

ADD REPLYlink written 3.8 years ago by mirza110

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).

ADD REPLYlink written 3.8 years ago by Jean-Karim Heriche22k
0
gravatar for Carlo Yague
3.8 years ago by
Carlo Yague5.0k
Canada
Carlo Yague5.0k wrote:

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.

ADD COMMENTlink modified 3.8 years ago • written 3.8 years ago by Carlo Yague5.0k
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