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Use DEG for meta-analysis

Hi everyone,

I heve some DEGs(differential expression genes) from RNA-seq analysis,I want to use Methods that combine p-value for meta-analysis in R.

-How I import DEGs, one by one or I should combine all DEGs for import and then do meta-analysis?

-does anyone know any template for preparation input,I mean what should be Rows and columns,only genes and p-value?

I choose MAMA package,could you give me some suggestions about another package?

Best Regards Elham

r
• 186 views • link
written by elhamdallalbashi • elhamdallalbashi

I'd just run the code in the vignette, and find out the structure of the 'ColonData' that they use; then munge my data into that format. Regardless, I'd probably use a random-effects model over the effect.sizes rather than p-values, especially if your input datasets are of different power.

... Then I'd write a tutorial explaining how I did the meta-analysis for bonus points

• 1 views • link
written by russhh russhh

You have micro-array data and DEG? MAMA is Somehow unfriendly package! do you know similar package specially designed for RNA-seq?

• 0 views • link
written by elhamdallalbashi • elhamdallalbashi

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