Here more NAs exist inside the calculated P-value and are classified as FALSE (non-contaminated features).

[YMSen]

Hello! We are conducting a study on microorganisms. We have found a large number of NA values for the final P-values when using decontam to identify potential contamination features. Could this be due to the presence of too many zero values in the data table? We have employed a negative control setting to identify potential contamination. Looking forward to your reply! Thank you for your help.

[benjjneb]

We have found a large number of NA values for the final P-values when using decontam to identify potential contamination features.

Any feature present in only 1 sample will get an NA score. My guess is that this explains your results.

[busihan]

Would you consider these features as contaminants because they only present in only 1 sample?

[benjjneb]

Would you consider these features as contaminants because they only present in only 1 sample?

I would consider these as features that do not have strong evidence supporting them as contaminants or non-contaminants.