Dear all, I am going to analyze some GSM from the GSE68379 from GEO. I need the gene expression from the cell lines that I will take in consideration (or the list of genes that are differentialy expressed among these cell lines). I have experience with the gene expression data for microarray analysis, but it's the first time that I work with methylated dataset. In details, I have these 2 troubles: 1. the current dataset doesn't present any differentiation by groups (normal, disease, etc) and all the cells I will consider are of the same kind (epithelial ovarian cancer), here is the question: how to make the model to produce the differentiated methylated regions? 2. supposed that I will solve the problem n.1 and get some results from the previous step obtaining a list of differentiated CpG, how to get the expression level of genes? It looks that this dataset doesn't publish this information ... or maybe that I don't know where to look.
Please guys, try your best to support me...I already spent many days without any acceptable results