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The error message seems clear: DESeq2 is intended for count data, and counts cannot be negative. You'll have to identify an appropriate statistical model and implementation for your data. This answer is necessarily vague because I don't know anything about your experiment or data. This online course (https://www.edx.org/xseries/data-analysis-life-sciences) and associated textbook (https://leanpub.com/dataanalysisforthelifesciences) introduce different linear models and their implementations in R/Bioconductor.