The choice of the filtering method in microarrays affects the inference regarding dosage compensation of the active X-chromosome.

When excluding the same proportion of transcripts as above (57.5%), but considering this time the X chromosome and autosomes separately, the difference of median expression levels between X-linked and autosomal transcripts became highly significant in both sexes (6.82 vs 7.91, P <10 −31 in males; 6.85 vs 7.91, P <10 −30 in females).

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