"Missing value where true/false needed" error with teGeneRetrieval about tissueenrich HOT 4 CLOSED

Hi Arun,

The problem is the value of maxNumberOfTissues argument. In your test data, the tissue number is 7 whereas for calculating group enriched genes you are using 7 (by default). If you change that to less than or equal to "max(tissues)-1", it will work. I have seen this issue before and planning to add a check in the teGeneRetrieval function. I hope this helps.

from tissueenrich.

Hi Ashish, thanks for the quick reply. Yes, that worked!
Related question: so if I'm using say 20 or more tissues, should I still use this maxNumberOfTissues one less than the total tissues or the default 7 is fine?

from tissueenrich.

I have put the default value (7) based on the Human Protein Atlas definition for the group-specific genes. The number depends on how you want to define the group-specific genes in your data. The "max(tissues)-1" check is just to ensure that code will not break when the maxNumberOfTissues >= max(tissues).

from tissueenrich.

I see. Okay, thanks for your help. I'm closing this issue.

from tissueenrich.