TAG, or bar-code, microarrays allow measurement of the oligonucleotide sequences (TAGs) that mark each strain of deletion mutants in the Saccharomyces cerevisiae yeast knockout (YKO) collection. Comparison of genomic DNA from pooled YKO samples allows estimation of relative abundance of TAGs marking each deletion strain. Features of TAG hybridizations create unique challenges for analysis. Analysis is complicated by the presence of two TAGs in most YKO strains and the hybridization behavior of TAGs that may differ in sequence from array probes. The oligonucleotide size of labeled TAGs also results in difficulty with contaminating sequences that cause reduced specificity. We present methods for analysis that approach these unique features of TAG hybridizations.