can I get a heat map from two groups of transcriptome data?

Question

[Kurban]

hello everybody,
i have a two group of RNA-seq data of an insect , one of them is control (not treated) another one is treated (low temperature) group. we assembled the raw reads and got unigenes, and did the related differential expression analysis (e.g. change fold=log2(treated/control)),then got many upregulated and down regulated transcripts.

now my questions are:
can i use these data to draw heat maps? if i could, how to do it (could u give me a brief approach )? could you also recommend some tools for windows or linux!?

Answer 1

[iraun]

Yes, you do a heatmap with these data. If you have a table with the FC values for each gene for each condition, you could have a heatmap with gene-names as rows and two column (control-treated).

There are different tools available to plot heatmaps. I usually use R, and inside R heatmap or heatmap.2 function. Here you can read some information and also some examples (https://stat.ethz.ch/R-manual/R-patched/library/stats/html/heatmap.html). Also in this link (http://flowingdata.com/2010/01/21/how-to-make-a-heatmap-a-quick-and-easy-solution/) you can find an easy tutorial.

Hope it helps.

[Farbod]

Dear @iraun, Hi

Which set of data is appropriate for heatmap drawing : fpkm , TPM, TMM, FDR or fold change ?

~ Take care