Bulk RNA-Seq Data That's Only Tumors (No Normal/Reference)?
Hi,
I have a dataset of only tumor samples and their raw counts, and I'm not really sure where to go from here. Can I run DESeq2 with only Tumors and no reference group? Should I be grouping the samples using clustering in order to use those are the different groups to run the analysis. I'm a little stuck. I really just want to look at which genes are more/less expressed and get some general insights from the data.
TIA!
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Answers/comments here encapsulate what you should be thinking about --> What Is The Proper Control Sample For A Tumor Rna-Seq Experiment?
Start with differential gene expression and possibly run through a deconvolution process after you group by cell type or by gene. Prior to that you would need RNA seq data to do anything and ideally sorted.
What are you talking about?
Maybe you could refer to some published datasets?
There is the problem: You do not tell what the scientific question is that you want to answer. Without knowing that one cannot advise what to do. It's the most critical thing to know!
I just want to look at which genes are being Differentially Expressed. Right now I am using K-means clustering to separate the groups and then run the analysis that way
Differential between what? "I just want to look..." is not a scientific statement. I can only help you if you clearly state what question you want answered.