how can we create heat map for only upregulated gene list
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
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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
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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).