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Hello, I have expression data from the cosmic database. I know how to work with edgR or DESQ2 packages in R to find differentially expressed genes between two conditions. But the Cosmic database gives a z score for each gene in different samples ( for each gene symbol it gives several z scores), so I can't work with the mentioned package. So now I’m searching for a method or package in r to give me DEG in R, That would be nice of you if you help me in this regard. thanks in advance for all suggestions
Afaik, COSMIC is a mutation database, they do not produced RNA-seq, meaning that the expression data came from other resources. See e.g. https://cancer.sanger.ac.uk/cosmic/help/expression
That having said, get proper data for your analysis, either via TCGA directly or via something like the Bioconductor packages Recount or TCGABiolinks.
First of all thank a lot for your answer. I know about the fact that cosmic database do not produced RNA-seq. But the point is that is there any package or way to use the z score from this database to do DEA or totally what can i obtain from it.
i have a dataframe with this information:
Zscore, gene name, cancer type,... in different samples.
Z-score is not suited for differential analysis. Get the counts from said resources and then use standard packages such as DESeq2 or limma-voom.