Hello,
I am currently using PLINK to perform a GWAS analysis for the MSBB-MSSM dataset; however, I can see that all of the AD status fields (column 6) are set to -9 or missing. Is this intentional? I did download the clinical data for this cohort, but a larger number of subjects in the FAM file (AMP-AD_MSBB_MSSM_IlluminaHiSeq2500_WES_QCed.fam) do not appear to have entries in the clinical dataset (AMP-AD_MSBB_MSSM_clinicalInfo_RNAseq_Dec2015_release.csv). Am i missing something? Ultimately, I would like to set all of the columns to the proper disease status.
Please see the file and link below.
https://www.synapse.org/#!Synapse:syn7535461
Thank you very much!
John
Created by John Malamon jmalamon Hi John, wanted to make sure that you are aware of the MSBB WES and RNAseq data update. See https://www.synapse.org/#!Synapse:syn2580853/wiki/409847
Hi John, sorry about the slow reply. You can map the WES files to the clinical covariates by using this WES covariate file (syn6101472) and this clinical file (syn6101474)