PRSice was used to calculate the PRS in ADNI dataset, but the results are quite abnormal ,see belows:
When I use the ADNI data in PRSice dir,the results R2 were quite large (eg:0.749622);
When I use the example data in PRSice dir,the results R2 were quite small (eg:0.0133696);
PRSice.prsice on ADNI
Set Threshold R2 P Coefficient Standard.Error Num_SNP
Base 0.0001 0.749622 8.43404e-23 56.3465 5.7326 33
Base 0.00015 0.829959 4.56913e-21 80.9499 8.59464 54
PRSice.prsice on example
Set Threshold R2 P Coefficient Standard.Error Num_SNP
Base 0.00025 0.0133696 8.43169e-06 -0.197266 0.0442903 2
Base 0.0003 0.00824473 0.000456434 -0.225204 0.0642503 3
1 answer
You are working on two different dataset, it is therefore normal that they are going to have a different result (different R2).
However, here, we have a special case where you've obtain an abnormally high R2 for your ADNI dataset. When it comes to PRS analysis, we usually expect a small R2, with a high R2, it is usually because you have use the same dataset to generate the GWAS summary statistic AND use the same set of sample to generate the PRS. You should make sure that an independent dataset is used to generate the GWAS summary statistics.
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I added
prsicetag, as I believe the developer of the program watches this tag.what do you mean by "add prsice tag", is this a parameter of the program?
Nope, he mean adding a tag to your post so that I can be notified.
Thank you for your advice~