I am a computer science master student and doing my final year thesis in applying AI in Oncology. In order to get the data for my ML models, my professor asked me to get the gene signature data for cancer and immune cells. For this, I have performed DEG analysis on the RNA-Seq data in R and got the required results with statistical properties. Now, my professor wants me to extract differentially expressed gene list for each of the samples provided i.e. individual list of genes for each sample. But, I am not sure how to extract the individual list of genes for each sample as I am new to Bioinformatics.
Also, I came across a post in Bioconductor support to extract the genes by using cutree function in R. I did use the cutree function which as follows,
## distance calculation of VST transformed DESeqDataSetFromMatrix obj gene_dist = dist(DESeqVST_Matrix) ## Hierarchical clustering gene_clust = hclust(gene_dist,method = "complete") gene_clusters = cutree(gene_clust,k=12)
Where K is the no. of samples i.e. 12 samples 6 in cancer and 6 in immune that gives each gene in different clusters, but I am not sure which cluster belongs to which sample.
I would be very pleased if you could guide me.