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GeneSCF and P-value Benjamini and Hochberg (FDR)

Dumb question about the GeneSCF output. If I'm using the P-value Benjamini and Hochberg (FDR) column, would I choose an FDR cut point and take any rows with a BH P-value less than this value as significant?

Thanks so much.

genescf
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updated by EagleEye EagleEye • written by aindap aindap

2 answers

I haven't seen the GeneSCF output but since FDR is used for multiple correction and I assume you are comparing many genes it makes sense to use all rows with an FDR value < 0.05.

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written by halo22 halo22

Hi,

In GeneSCF if you are choosing FDR cutoff of 0.05, then whatever entries less than 0.05 is significant and take those rows (Same applies if you consider only P-values for filtering).

My suggestion (Again it depends on your dataset/experiment): Since GeneSCF also considers terms containing entries with only one or two genes in the database, in addition to P-values/FDR I would also prefer to use minimum number of genes to consider ('num_of_genes' column) as filter criteria from the output.

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written by EagleEye EagleEye

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