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fold-change and FDR p-value threshold for miRNA (small RNA-Seq) data

HI, I am analyzing miRNA (small RNA analysis) data and I would like to establish a fold-change and p-value threshold which is biologically significant.with Fold change ≥ 1.5 and FDR P-VALUE ≤ .05, I lose most of miRNA.

rna-seq
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updated by kanwarjag kanwarjag • written by Edalat • Edalat

1 answer

Fold change may not be best as some microrNAs will have zero values in one case while very large value in another case. you can still calculate the FC by transforming values, but I think p value may be best, you can use DEseq, EdgeR or even simple t test.

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written by kanwarjag kanwarjag

thank you for attention. with FDR P-VALUE ≤ .05 of t-test (without fold change) , I lose most of miRNA too, I think to use bigger p value?

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written by Edalat • Edalat

Then I will see how many replicates you have. It looks like you have few replicates and which do not show a good correlation with in a group

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written by kanwarjag kanwarjag

excuse me which is better for filtering miRNA ,FDR P-value or P-value?

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written by Edalat • Edalat

I read many things about being cautious with p-value then I prefer FRD

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written by zizigolu zizigolu

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