I simply wanted to compare differentially expressed genes between 2 types of tissues using RNA-seq. Following, data was processed by a Bioinformatics person and provided 2 types of Excel files:
1. Normalized read count (tissue-A and -B)
2. Differentially expressed transcripts (tissue-A and -B). This contained columns including ( Gene Name, Base Mean, log2 Fold Change, lfcSE, stat, pvalue and padj)
Unfortunately, the person didnt generate any presentable graphics including heatmaps or Venn diagrams etc. and has left job. I am new to this so need help:
1. How can I generate heatmaps or Venn diagrams or other suitable diagrams suitable for comparing differentially expressed genes between the two tissues?
2. How can I use differentially expressed genes in Excel file to represent this data in graphical format?
The most user-friendly way to process your data would be Galaxy. Just sign up and upload the data. You will find tutorials regarding generating heatmaps and different plots, just google it.
https://usegalaxy.eu/
Let me know if you need any help.
The most common visualization for these types of analysis is the Volcano plot (https://en.wikipedia.org/wiki/Volcano_plot_%28statistics%29). You will need some stats software to visualize it. Here's an example in R: https://www.r-bloggers.com/using-volcano-plots-in-r-to-visualize-microarray-and-rna-seq-results/
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