Question: p-value and adjusted p-value exactly the same
1
gravatar for mimA
2.4 years ago by
mimA30
European Union
mimA30 wrote:

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!!!

microarray R • 1.3k views
ADD COMMENTlink modified 2.4 years ago by Dan Gaston7.1k • written 2.4 years ago by mimA30

see my post here on this topic http://crazyhottommy.blogspot.com/2015/03/understanding-p-value-multiple.html

ADD REPLYlink written 2.4 years ago by Ming Tang2.4k
5
gravatar for Devon Ryan
2.4 years ago by
Devon Ryan89k
Freiburg, Germany
Devon Ryan89k wrote:

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 COMMENTlink written 2.4 years ago by Devon Ryan89k

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 REPLYlink written 2.4 years ago by mimA30
4

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 REPLYlink written 2.4 years ago by russhh4.3k

ok, will use Limma, thank you!!

ADD REPLYlink written 2.4 years ago by mimA30

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

ADD REPLYlink written 2.4 years ago by John12k

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

ADD REPLYlink written 5 days ago by Researcher10

Please create a new post.

ADD REPLYlink written 4 days ago by Devon Ryan89k
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