search

YuLab-SMU / biomedical-knowledge-mining-book

:books: Biomedical knowledge mining using GOSemSim and clusterProfiler
https://yulab-smu.top/biomedical-knowledge-mining-book/
69 stars 27 forks source link

How to compare two conditions ? #10

Open Bio-data-tricks opened 2 years ago

Bio-data-tricks commented 2 years ago

Hello everyone, I have affymetrix data with gene annotation. I would like to compare a control sample (n=3) vs another condition (n=3). Could someone help me to use enrichplot and clusterProfiler to visualize the differences between these two samples? Which functions should I use ?

Thank you !

Nicolas dat.xlsx

DaiqingChen commented 2 years ago

Hi Nicolas, I am also just a user of clusterProfiler, not the authors. But from my experience, you should first choose your differential expressed gene list, the most common criterial is adjusted P-value < 0.05 and logFC >1. A tutrial you can follow: [https://www.bioconductor.org/packages/devel/workflows/vignettes/RNAseq123/inst/doc/limmaWorkflow.html]

Then annotate these differential expressed genes by GO or KEGG, as Chapter 6 and 7 from the book. After that you will be able to visualize the difference. There is no one single function you can run to get the plot.

Best, Daiqing