Missing values

[FarmOmics]

Missing values

[francois-a]

No, only missing genotypes are automatically imputed (to the mean). This isn't built-in for phenotypes, since the appropriate imputation will depend on the phenotype and reason for missing values.

[FarmOmics]

As my phenotypes have missing values, I am wondering how we can process those missing values? Can we set missing values as "-9" or "na" when we run tensorQTL?

[francois-a]

You'll need to impute the missing values (e.g., with the mean, or half-minimum value, etc., before inverse normal transform). The appropriate imputation will depend on the phenotypes -- what are your phenotypes?

[Geneva0725]

Hi, I have the same problem and I'm going to discovery eQTL from single cell RNA-seq dataset based on droplet platform. There are many NAs in my data, like 10% NA within a single feature(gene), and I'm wondering which imputation method should be appropriate, btw, there are around 400 samples in my data.
And I'm wondering what if I make NA to be 0 after inverse normal transform, is that OK?

Thanks!