Question: how can we create heat map for only upregulated gene list
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gravatar for anjanasoman007
14 months ago by
anjanasoman0070 wrote:

how can we create heat map for only upregulated gene list for FPKM treated vs control? I am getting two solid color for treated and control resp not gradient color

rna-seq • 471 views
ADD COMMENTlink modified 14 months ago by Antonio R. Franco4.1k • written 14 months ago by anjanasoman0070

what is the criteria for upregulation? If you are using fc/lfc, use a cut off to filter the data frame for upregulated data. Then use one of the heatmap plotting libraries (heatmap2 from gplots, complexheatmap, pheatmap, heatmap3 etc).

ADD REPLYlink written 14 months ago by cpad011212k
0
gravatar for Antonio R. Franco
14 months ago by
Spain. Universidad de Córdoba
Antonio R. Franco4.1k wrote:

You need to filter your data. There is not mention to the method you got your data, but you can use R, excel and many other programs to filter

ADD COMMENTlink written 14 months ago by Antonio R. Franco4.1k
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