50000 significant p values
1
0
Entering edit mode
7.2 years ago
chowdhury • 0

I have ADNI microarray dataset (https://ida.loni.usc.edu/pages/access/geneticData.jsp#207). The paper says it is normalized data. I have used R -limma package to do the expression analysis among healthy controls and patients. It has around 50000 probe set and sample size of 700 (equal amount of control and patients). After the analysis, all 50000 probe ids showed high significance level (<0.01). Is it possible?

R microarray pvalue • 1.6k views
ADD COMMENT
0
Entering edit mode

What p-value correction did you apply (if any)?

ADD REPLY
0
Entering edit mode

Is this normal?

No.

But you'll need to add more information to this question in order to get accurate troubleshooting, such as which technology, which experimental setup, which packages, which code,...

ADD REPLY
0
Entering edit mode

I have ADNI microarray dataset (https://ida.loni.usc.edu/pages/access/geneticData.jsp#207). The paper says it is normalized data. I have used R -limma package to do the expression analysis among healthy controls and patients. It has around 50000 probe set and sample size of 700 (equal amount of control and patients). After the analysis, all 50000 probe ids showed high significance level (<0.01). Is it possible

ADD REPLY
0
Entering edit mode

Is it possible

No.

all 50000 probe ids showed high significance level (<0.01)

Are all transcripts up- or downregulated or both directions?

The paper

Which paper? Be specific.

And please use ADD REPLY to answer to earlier comments, as such this thread remains logically structured and easy to follow.

ADD REPLY
1
Entering edit mode

@chowdhury Are you sure you are dealing with gene expression data? The link you have given says geneticData.

The only information I can find about ADNI mentions only genotyping arrays. http://adni.loni.usc.edu/methods/genetic-data-methods/

and the following 2010 paper about the Alzheimer's Disease Neuroimaging Initiative also mentions only Illumina genotyping arrays.

/https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2868595

ADD REPLY
0
Entering edit mode
7.2 years ago
kloetzl ★ 1.1k

Judging from your comment you did not apply any p-value correction. As you are doing multiple tests, you have to change your acceptance level from 0.01 to 0.01/50000 in the simplest case (Bonferroni). That then is the true alpha-value you have to compare with.

ADD COMMENT
6
Entering edit mode

Bonferonni is not appropriate (too stringent) for gene expression analysis. In addition I would expect Limma to perform multiple testing correction.

ADD REPLY
2
Entering edit mode

I agree, False Discovery Rate (FDR) in limma is appropriate.

ADD REPLY

Login before adding your answer.

Traffic: 1589 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