"AssertionError: Covariate ids and Y ids don't match."

[Sandyyy123]

Hi,
Please help to resolve the isssue.
I used MAGMA output directly from FUMA to run the analysis using gene_annot_jun10.txt provided in your example dataset. The file works perfectly with your example MAGMA output of PASS_SCHIZOPHRENIA though.
Thanks.

[tongshiyuan]

Hi, Please help to resolve the isssue. I used MAGMA output directly from FUMA to run the analysis using gene_annot_jun10.txt provided in your example dataset. The file works perfectly with your example MAGMA output of PASS_SCHIZOPHRENIA though. Thanks.

Hi, I have encountered the same problem. I think it may be due to the gene ID. Trying to convert the "ENTREZID" in your MAGMA database to "ENSEMBLID" should solve this issue.

[kllrdr]

Hi @tongshiyuan , I found the same issue. I converted the IDs, but then I lost some genes during the process, since I do not have ENTREZID from all genes. Also, MAGMA has another output, the matrix file .raw, which I need to use to run the analysis. It includes a column with correlation data between the different genes. Is there a way to delete the genes that are not present in the gene annotation file from pops_features? I can delete the non-matching gene rows from the matrix, but then the correlation values with the deleted genes still remain. How did you deal with this issue?