This is a test version of Biostars. For the public version, visit https://www.biostars.org.
p-value and adjusted p-value exactly the same

Hi all,

I'm analysing some microarray data and just calculated p-values using a t-test between 2 conditions (each with 3 replicates; total number of genes 14000). My p-values and adjusted p-values are coming out exactly the same. I've tried both FDR and bonferroni for correction using the p.adjust function in R and the results are the same. Is it possible to have the exact same p-values and adjusted p-values. I'm getting a bit doubtful. Any thoughts.

Thanks!!!

r microarray
• 6,687 views • link
updated by DG DG • written by mimA • mimA

1 answer

It's impossible to have the same p-value and adjusted p-value after bonferroni correction with 14000 genes. There must be an error with the code at some point, please post it.

Also, you want to use limma rather than directly doing a T-test.

• 0 views • link
written by Devon Ryan Devon Ryan

Hi Devon, Thanks for your answer! You were right there was an error in my code somewhere. I fixed it so now the 2 values are not the same. About your comment on using Limma. I didn't exactly follow. You don't think using just a simple t-test and then adjusting for multiple comparisons is advisable? I used the Affy packages for QC and normalisation.

• 0 views • link
written by mimA • mimA

limma is the GOTO package for microarray analysis. limma borrows information across multiple genes to better estimate the variability for a given gene, it provides a more powerful test that the naive t-test would.

• 0 views • link
written by russhh russhh

ok, will use Limma, thank you!!

• 0 views • link
written by mimA • mimA

In general, a test + post-hoc correction is never as good as using a multivariate test to begin with.

• 0 views • link
written by John John

Hi mimA, Can you please share the correct syntax for p value correction, as I am also facing the same issue.

• 0 views • link
written by Researcher Researcher

Please create a new post.

• 0 views • link
written by Devon Ryan Devon Ryan

Log in to answer this question.

More posts like this