Question: Using DESeq2 to analyze similarities in treatment effect - 2 conditions and 4 genotypes
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17 months ago by
martin.strand0 wrote:

I have a mRNASec dataset with 2 conditions and 4 genotypes and I'm interested in finding genes that have a similar change in expression across the 4 cell lines in response to the treatment, while taking differences in genotype into account.

experiment: condition: treated, control genotypes: 1, 2, 3, 4

When using DESeq2 to look at condition effect with the design formula: ~ condition, the result is, as far as i understand, a comparison of all treated samples versus all control samples without taking genotype into account. By using interaction terms, as suggested in the ?results, it is possible to compare the condition effect between two genotypes. Is there however a way to compare similarities in condition effect across the 4 genotypes in DESeq2?

I'm considering doing an ANOVA analysis of log2fold change values across the 4 genotypes.

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