p-value and adjusted p-value exactly the same
1
1
Entering edit mode
4.4 years ago
mimA ▴ 30

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 • 2.7k views
ADD COMMENT
0
Entering edit mode
ADD REPLY
5
Entering edit mode
4.4 years ago

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.

ADD COMMENT
0
Entering edit mode

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.

ADD REPLY
4
Entering edit mode

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.

ADD REPLY
0
Entering edit mode

ok, will use Limma, thank you!!

ADD REPLY
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode

Please create a new post.

ADD REPLY

Login before adding your answer.

Traffic: 1874 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6