Question: can I get a heat map from two groups of transcriptome data?
0
gravatar for Kurban
3.9 years ago by
Kurban170
china/Urumqi/xinjiang academy of animal scinces
Kurban170 wrote:

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!?

heat map • 2.3k views
ADD COMMENTlink modified 3.9 years ago by iraun3.5k • written 3.9 years ago by Kurban170
2
gravatar for iraun
3.9 years ago by
iraun3.5k
Norway
iraun3.5k wrote:

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.
 

ADD COMMENTlink written 3.9 years ago by iraun3.5k

Dear @iraun, Hi

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

~ Take care

ADD REPLYlink written 2.4 years ago by Farbod3.2k
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