Dear RG community,
I have a dataset composed by 100 samples of Acute Lymphoblastic Leukaemia Patients sequenced by Illumina Tru-Sight RNA PanCancer - Target Capture Next Generation Sequencing ( 1384 targeted genes involved in oncogenic processes), and I would like to perform Differential Expressed Genes Analysis within this dataset. I would like to ask you for the feasibility of the idea and its pitfalls.
Thank you,
Best,
Andrea
Hi Andrea,
You can use such dataset for differential expression analysis, this is no problem. Although to do that, you need the groups inside your dataset - for example you can compare cancer patients vs healthy control patients. I guess that most of the NGS-related cancer studies appeal to the healthy controls in the DE analysis.
The limitation to 1384 cancer-related genes though will make a bias towards Cancer-related gene ontology terms if you decide to run the list of DE genes through the GO analysis or Gene-set-enrichment or similar. So you need to be cautious about that.
Best,
Michail
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