DESeq2 Result Files

A DESeq2 result file (*.deseq.res.csv) is a CSV file containing a header row followed by one row for each gene or transcript. The first column contains the gene or transcript ID. The other columns are:

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GeneName—Gene name for gene level results or transcript ID for transcript level results.

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baseMean—The average of the normalized count values, dividing by size factors, taken over all samples.

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log2FoldChange–The effect size estimate. This value indicates how much the gene or transcript's expression seems to have changed between the comparison and control groups. This value is reported on a logarithmic scale to base 2.

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lfcSE–The standard error estimate for the log2 fold change estimate.

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stat–The value of the test statistic for the gene or transcript.

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pvalue–P-value of the test for the gene or transcript.

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padj–Adjusted P-value for multiple testing for the gene or transcript.

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status–Low if baseMean is less than or equal to filterThreshold calculated by DESeq2 for the gene or transcript. OK for all the other genes or transcripts.

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control–Expression of the control group back-calculated from baseMean and log2FoldChange. NA if log2FoldChange is not available.

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comparison–Expression of the comparison group back–calculated from baseMean and log2FoldChange. NA if log2FoldChange is not available.