Missing value estimation methods for DNA microarrays

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Troyanskaya, O., Cantor, M., Sherlock, G., Brown, P., Hastie, T., Tibshirani, R., Botstein, D., and Altman, R. B. (2001). Missing value estimation methods for dna microarrays. Bioinformatics, 17(6):520–525. 10.1093/bioinformatics/17.6.520


SVD, KNN and row average imputation are evaluated with different parameter settings on real data sets with regard to robustness, sensitivity and accuracy.

Study outcomes

Outcome O1

Rank of performance: KNN, SVD, row average, zero filling.

Outcome O2

"KNN is relatively insensitive to .. K within the range of k=10-20" (Figure 1)

Outcome O3

SVD "is sensitive to the type of data" and "is ideally suited .. in terms of .. constituent patterns"

Study design and evidence level

Just 4 imputation algorithms (SVD,KNN) are evaluated from which 2 are singular value substitutions (average,zero).

Analysis is performed over a broad range of hyperparameters (KNN: k=[1,1000], SVD: Eigengenes=[5,30]).

The imputation methods are only analyzed on data with less than 20%.