I have 80 rna-seq datas from different tissue at different treatment. After Tophat and Cufflinks, i retrieve each gene's fpkm from gene.fpkm_tracking file produced by cufflinks. There is about 20,000 genes in one sample.
I have no ideas to visualize the data in a clear, comprehensive way. I want to display these data in one graph. Any advice is appreciate! Thanks in advanced!
What is it you want to visualize? Do you want to visualize how samples can be classified based on expression markers? Then try a unsupervised hierarchical clustering heatmap of the 500 genes with the most variance across all your samples. Do you want to visualize what sample groups there are in your data? Make a 3d scatter plot of the first 3 principal components (PCA-analysis). Or do you want to visualize the genes that are differentially expressed across the samples? Use these genes to make a clustering heatmap
Thank you for your reply! I just want to visualize the distribution of 20000 genes' fpkm value from 80 pieces of data. I will try 3d scatter plot of sample, fpkm and gene id.
Sounds like a heatmap would work for you.
If you want to see the distribution of fpkm values in each sample you want to make a histogram/1d density plot of the logged (!) fpkm values of each sample. That way you will get a feel about what the mean, median, variance, minimum and maximum fpkm values you have in each sample. To me, it sounds like you do not exactly know what you want with the data. I advice you to very clearly set your goals. Begin with very high level goals and define more specific subgoals