Differential expression graphics

[Chuckytah]

Hello all,

I wanna do this type of graphic:
http://www.jimmunol.org/content/172/...0/F1.small.gif or http://www.omicsonline.org/2157-7099...1-101-g005.gif

but i'm kind noob in this field... what should be the type of my data?

i have something like this:

library/condition geneA geneB geneC
I 2.0 1.6 12.0
II 13.0 1.4 0.4
III 17.0 1.3 0.3

I use percentages... so for example i know that geneA is more expressed in the III condition, etc... right?

How can i do a graphic like that one above? sorry my poor english.

[vineeth_s]

Hi Chuckytah,

The images you refer to, are what are called Heat Maps

For your kind of data, this will have to be done in 2 steps:
1. Generate clusters using software like Michiel de Hoon's Cluster
2. With the files generated there you can use Java TreeView to generate the heat maps

Good luck

[essvee]

In R there is fairly an easy to use function called heatmap that will allow you to do this.
You can play with scales, colours, and formatting.
Hope this helps.

[Chuckytah]

In R there is fairly an easy to use function called heatmap that will allow you to do this.
You can play with scales, colours, and formatting.
Hope this helps.

The function is called "heatmap" ? but it there is no need to install a certain package?

ty

[Chuckytah]

Hi Chuckytah,

The images you refer to, are what are called Heat Maps

For your kind of data, this will have to be done in 2 steps:
1. Generate clusters using software like Michiel de Hoon's Cluster
2. With the files generated there you can use Java TreeView to generate the heat maps

Good luck

Thanks a lot. I download those programs i will try later

[steven]

The function is called "heatmap" ? but it there is no need to install a certain package?

ty

I once used one called "image" to generate a 2D heatmap in R-please don't ask me why not "heatmap".

[essvee]

The function is called "heatmap" ? but it there is no need to install a certain package?

ty

I do not believe you need to install any additional packages. It should be included in your standard installation.
There are a lot of tutorials floating around, I would suggest searching to find the one most relevant to the type of data you are analyzing.
Hope this helps

[Simon Anders]

I once used one called "image" to generate a 2D heatmap in R-please don't ask me why not "heatmap".

The difference is that heatmap rearranges the rows and columns of your matrix by clustering and adds dendrograms, and image does not.

[steven]

The difference is that heatmap rearranges the rows and columns of your matrix by clustering and adds dendrograms, and image does not.

Ah, thanks Simon, I did not remember that. Yes, my matrix had to be plotted "as is", so it makes sense indeed.

[themerlin]

The multi experiment viewer generates heatmaps in one easy step. Those graphics you sent look like they were made in MeV.

http://www.tm4.org/mev/

[Chuckytah]

I know that heatmaps can be made on R, but my R is not working, dunno why, can't install new packages, maybe because of university proxy.

I have done one using Matlab, but it is not so well I think...

I will try MeV so