Query for limma and DEseq2

2

Hi
I want to show the common differentially expressed genes from two data set.One is affymatrix data and the other is RNAseq dataset from GEO.For that atfirst i have to analyze the dataset individually.So will i can analyze affymatrix data with limma and the RNAseq data with DEseq2.I want to know ,will this logical or I have to analyze both with the same package??


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