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Nigussie Tadesse
Mar 12, 2023, 11:47:33 PM3/12/23
to FUMA GWAS users
Dear FUMA developer team
Job ID: 237320
May I have your explanation on how can I download the identified genes from the result table of the MAGMA gene-set analysis? The magma.gsa.sets.genes output text file only shows the first row of the gene set analysis table even though there are 10 rows.
Thank you for the wonderful software.
Regards,
Tanya Phung
Mar 13, 2023, 5:56:30 PM3/13/23
to FUMA GWAS users
Hello,
In the table, there are 10 rows because these represents the top 10 gene sets with the lowest p value. However, some of these sets are not significant after Bonferroni correction.
The reason why you only see the genes for 1 gene set in the downloaded file magma.gsa.sets.genes is because only one gene set was significant (adjusted pvalue < 0.05) after Bonferroni correction.
In order to verify this, you can calculate the adjusted p value (by Bonferroni) from the output file magma.gsa.out. Then, you will see that only 1 gene set is still significant after applying Bonferroni correction.
I hope this answer makes sense.
Best,
Tanya
The reason why you only see the genes for 1 gene set in the downloaded file magma.gsa.sets.genes is because only one gene set was significant (adjusted pvalue < 0.05) after Bonferroni correction.
In order to verify this, you can calculate the adjusted p value (by Bonferroni) from the output file magma.gsa.out. Then, you will see that only 1 gene set is still significant after applying Bonferroni correction.
I hope this answer makes sense.
Best,
Tanya
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