pred_perf_r2,pred_perf_pval.pred_perf_qval are always NA about metaxcan

[empathy-c]

I then would like to know how to interpret the results obtained from running spredixcan.py and smultixcan.py. What criteria should be used to determine the association between genes and phenotypes?

[ahasuni]

Hi there,

Did you figure out the NA issue? I am running SPrediXcan and am also getting all NAs in pred_perf_r2,pred_perf_pval.pred_perf_qval columns. I am running the program for multiple traits and tissues and its the same result for all of them. Roughly 87% SNPs are included in model.

hasuni

[Fnyasimi]

Hi @empathy-c @ahasuni the pred_perf_r2,pred_perf_pval.pred_perf_qval are metrics of the model when it was trained and not metrics from your S-PrediXcan results. The summary file just gives more information about the model, you should focus on the prediction results with pvalues and zscores