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KlugerLab / ALRA

Imputation method for scRNA-seq based on low-rank approximation
MIT License
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Final proportion of non-zero values is large. #20

Open ayeTown opened 2 years ago

ayeTown commented 2 years ago

I start with a matrix which has 10.81% nonzero values. After using this imputation method this proportion changes to 55.95%. Is this reasonable compared to your experiments?

Rohit-Satyam commented 1 year ago

Hi @ayeTown. I also observe this. When using all samples together via merging their count matrices and then performing imputation, I observe increment of non-zero values from 0.5% to 17% only. However, if I separately impute them they go as high as 50%. Did you get any method to gauge if ALRA is performing over-imputation or not?

yamihn commented 1 year ago

I faced the same. Any solution?