How to use simpleM result?

kayeee_ — Fri, 19 Jan 2024 06:40:02 GMT

Hello. I am trying to analyze over 300 SNP(single nucleotide polymorphisms)s data

I came across information suggesting the use of corrected P-values (MultipleM) for SNP data's P-values.

I found a code implementation in the provided URL (9 pages - 3.2 Alternative to Proc PSMOOTH),

https://support.sas.com/resources/papers/proceedings09/240-2009.pdf

The example result is shown below.

7 parameters explained 99.5% of All parameters.

How should I set the corrected P-value?

Is it 0.05/7, 0.05/340, or is there another approach?

Proportion	Cumulative	Meff	alphaG
0.5193	0.5193	.	.
0.2424	0.7617	.	.
0.1547	0.9164	.	.
0.001	0.9174	.	.
0.005	0.9224	.	.
0.0154	0.9378	.	.
0.0572	0.995	7	0.007143
0.0004	0.9922	8	0.00625
0.00004	0.99224	9	0.005556
…	…	…	…
0	1	300	0.000147

Re: How to use simpleM result?

sbxkoenk — Fri, 19 Jan 2024 08:42:47 GMT

Hello,

I looked at page 9

https://support.sas.com/resources/papers/proceedings09/240-2009.pdf

SAS Global Forum 2009 -- Paper 240-2009
Beyond SAS/GENETICS™
Amina Barhdadi, Yassamin Feroz zada, Marie-Pierre Dubé
Montreal Heart Institute and Université de Montréal, Montreal, Canada

The code is clear.

... ...
 If cumulative>0.995 then Meff=number; /* cumulative and number are two provided variables in eigenvalues data set*/
Run;
/*Step4-Apply the Bonferroni correction formula to adjust point-wise significance level*/
Data Meff;
 Set Meff;
 alphaG=alphaE/Meff; /*alphaE is the experiment-wise error rate*/
Run;

Meff is an estimate of the effective number of independent tests.
In your use case Meff = 7 , so you divide the test-wise error rate by 7 to get the experiment-wise error rate (Bonferroni correction). Like 0.05 / 7 = 0,007143 .

Important Note:
The last comment line says : /*alphaE is the experiment-wise error rate*/

The experiment-wise error rate is on the left-hand side of the equality sign of course.

What you divide by 7 (Meff) is the test-wise error rate.
So, the comment is wrong (should say alphaG) ... or alphaG and alphaE should switch places.

Koen

topic How to use simpleM result? in Statistical Procedures

How to use simpleM result?

Re: How to use simpleM result?