I have downloaded dataset from GEO datasets and and in toptable I got 22,000 genes in it with logFC value and adj. p value. I got the gene symbols as well. But I have to find upregulated genes and downregulated genes. CAn someone tell me how should I find up/down regulated genes from the list of DEGs.
Please provide more info when you ask a question, it helps us to answer you. What dataset are you looking at, and what samples/groups are you comparing?
I am assuming you have assigned the samples in the dataset to different groups for analysis using the GEO2R website? If you have compared two groups then the resulting logFC is the log fold change between those groups and there should be a volcano plot in the output. For example if we have compared tumour (group A) vs normal (group B), the volcano plot will show you the genes that are up-regulated and down-regulated in the normal samples (group B). I found this through google which explains differential gene expression volcano plots quite nicely:
This information is also indicated by the sign of the values in the logFC column. Positive values are up-regulated genes, negative values are down regulated in group B compared to group A. Hope this helps.
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Nat.Nataren I got your point. Thankyou so much for sharing this. And Yes I was doing tumor vs control group.
Not a problem, happy to help :)