Entering edit mode
3.2 years ago
jdhindsa1999
▴
20
Hello,
I am hoping to receive some guidance on interpreting an RNA-sequencing project I am conducting. For this project, I have 9 time points, 3 biological replicates per time point, and 2 genotypes: wildtype vs mutant. I am using a likelihood ratio test in DESeq2 using the following code:
dds <- DESeqDataSetFromMatrix(ctdata, coldata, design = ~ genotype + age
dds <- DESeq(dds, test = 'LRT', reduced = ~ age)
From a DESeq2 training page, the log2 fold change is printed in the results table for consistency with other results table outputs, but is not associated with the actual test. However, I am interested in detecting upregulated and downregulated genes. Seeing as I cannot use the log2 fold change from the DESeq results to do so, does anyone have any advice on how to go about this?
