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Old 09-15-2011, 12:19 AM   #1
lynn012
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Location: china

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Default How to calculate P-value&FDR

Hi,
When I analyse the significance of gene expression profiles, I should calculate the P-value&FDR. But I don't know how to calculate.Grateful for answers.
Thanks!
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Old 09-15-2011, 05:48 AM   #2
dariober
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Quote:
Originally Posted by lynn012 View Post
Hi,
When I analyse the significance of gene expression profiles, I should calculate the P-value&FDR. But I don't know how to calculate.Grateful for answers.
Thanks!
Hi,

If you are talking about a microarray experiment have a look at the R/Bioconductor package limma. If it is next gen data (RNAseq, Chipseq) see the packages edger or deseq. If instead you want to convert a vector of p-values to fdr values see the function p.adjust in R.

(A suggestion... I think you should make your questions a bit more detailed for people to help!)

Dario
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Old 09-18-2011, 10:51 PM   #3
lynn012
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Dario,
Thanks for your help and I will make my questions a bit more detailed in the future. My data is next gen data(DGE). Thanks for your timely answer and patient explaination again!
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