DESEQ2 Formula with 5 variables
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Bine ▴ 10
@bine-23912
Last seen 5 weeks ago

Dear all,

I believe I am using the DESEQ2 Formula correct but after getting some unexpected results I would like to double check with you:

I want to check the effect of Vitamin D on patients and I have a group who takes Vitamin D and a group who doesn't take Vitamin D. Since these groups are quite different I need to adjust for Gender, Age, Batch and BMI.

My formula is:

dds <- DESeqDataSetFromMatrix(countData = cts, colData = colData, design ~ batch + Gender + Age + BMI + Vitamin_D_Group

I understand that I need to put the factor I want to analyse at the end and the other variables I am adjusting for in the beginning of the formula, following this "With no additional arguments to results, the log2 fold change and Wald test p value will be for the last variable in the design formula, and if this is a factor, the comparison will be the last level of this variable over the reference level".

Can anyone confirm me that this is correct?

Thank you so much, Bine

DESeq2 • 197 views
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@mikelove
Last seen 13 hours ago
United States

I don't understand the question. You're asking if the vignette recommendation is correct? Yes, this is correct.

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The question is if I put it correctly in my formula so that i will adjust for batch, Gender, Age, BMI and do the Differential expression for Vitamin D Group?

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Yes, this is how we correct for multiple terms in linear models.

However, I will note that if you don't have a balanced design and you throw lots of variables in the design, you can have diminished power. But that has nothing to do with DESeq2.

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Thank you for your answer.

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