hi, there.

i am working on the RNA seq data analysis and i both use the R package DEGseq and edgeR to obtain DEGs .however, the DEG lists i get from these two packages are not much alike.

here is the total number of DEGs i get:

No code has to be inserted here.and the total matched gene is about 17380(71.40%) in dataset 1 and 16000 (65.72%) in dataset 2respectively.

and DEGs filter threshold are : FDR <=0.001, |log2 FC|>1

i am confused now and i just want to know which one is more reasonable?

i am working on the RNA seq data analysis and i both use the R package DEGseq and edgeR to obtain DEGs .however, the DEG lists i get from these two packages are not much alike.

here is the total number of DEGs i get:

No code has to be inserted here.and the total matched gene is about 17380(71.40%) in dataset 1 and 16000 (65.72%) in dataset 2respectively.

and DEGs filter threshold are : FDR <=0.001, |log2 FC|>1

i am confused now and i just want to know which one is more reasonable?

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