CODEWITHSUNDEEP
parametersstatisticsbioinformaticsp-value
Cinmoyee
Cinmoyee

Reputation: 1

What parameter and threshold to choose to get significant pathways from MetaboAnlyst pathway analysis results?

MetaboAnalyst pathway analysis results give a total of 4 different p-values viz, raw p-value, -log10 pvalue, Holm-Bonferroni adjusted p-value and the FDR value. And an impact score.

Which value should be considered in my case (image link below) to get significant pathways? And what should be the threshold cut off?

Click here for Pathway results image

I tried to choose based on raw p-value< 0.05

Upvotes: -1

Views: 35

Answers (1)

Laura Budurlean
Laura Budurlean

Reputation: 21

I would go with the FDR adjusted P-value. The false discovery rate adjusted value is a less conservative approach compared to traditional methods, like the Bonferroni correction, but I would never go with the raw P-value especially if you are querying for hundreds/thousands of pathways.

Upvotes: 0

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