Condition shown as 'Untreated vs. Treated' in output of results() in DESeq2
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treebig44 ▴ 30
@bffcbc5f
Last seen 5 weeks ago
United States of America

I am trying to find differentially expressed genes using DESeq2 on some RNA-seq data. In the pheno data, there is a column named 'condition' with factored values of 'Treated' and 'Untreated'. I want to use just this column for my experiment.

However, when I use the results() function in DESeq2 with my data, I get the first line as: 'log2 fold change (MLE): condition Untreated vs Treated'

Now, I am new to this, so I am not sure if this is the same as 'Treated vs Untreated' or not. And I don't know why it decided to show 'Untreated vs Treated'.

I would love some clarification. Are the 2 things (A vs B and B vs A) the same? If not, what does each one mean? and how to control what is compared?

exp_1 = DESeqDataSetFromMatrix(
countData = Counts,
colData = Phenotypic[match,],
design = ~ condition
)

my_deg = DESeq(exp_1)

fin_results = results(my_deg, alpha=0.05)

RNASeqData DESeq2 • 141 views
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I have understood that the difference is in the swapping of the numerator and the denominator during the calculation of log2FC. But would still like to know how this affects my results, and how to control this.

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@mikelove
Last seen 4 hours ago
United States

This is covered in the vignette (note on factor levels).