gravatar for K.patel5

2 hours ago by

Hi Biostars,

I have performed differential expression (DE) on microRNA-seq data. Unlike RNA-seq data, this is quite small; I only have 1978 genes across X samples. I believe this is why I am running into issues when interpreting the DE results.

The standard for RNA-seq analysis is to use adjusted P values which have been corrected based on the number of genes found. Usually from an RNA-seq analysis we would expect between 20-40,000 genes. Adjusted P values are valuable here and are now seen as a mandatory check used when discussing results.

Meanwhile in the world on microRNAs, we must do with usually < 2,000 genes. Here are my lowest 3 adjusted P.values from contrasting 30 disease samples / 16 non-disease samples -- so plenty of replicates.

                       lof2fc        P value          adjusted P value
mmu-miR-375-3p         3.589905e-01  6.472503e-06     0.007805839
mmu-miR-200b-3p       -7.077764e-03  9.997980e-04     0.602878205
mmu-miR-429-3p         4.179860e+02  1.513482e-03     0.608419692

As such my question is, for miRNA-seq analysis are adjusted P values unnecessary because we lack the number of genes to perform multiple correction testing adequately?

Appreciate any insight.

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