Hi valued researchers,
I may ask a question on how to extract the results of DESeq2. my design was: dds <- DESeqDataSetFromMatrix(countData = countData, colData = colData, design = ~ category + gender + age + BMI + weight_kg) dds <- DESeq(dds) Then, to extract genes explined by age, BMI, and Weight, I did as follow for each and got up/down regulated genes ddsBMI <- dds design(ddsBM) <- formula(~ ddsBMI) ddsBM<- DESeq(ddsBM) res <- result(ddsBMI)
However, I got zero up and down-regulated genes for each variable when I used res <- results(dds, name="BMI") res <- results(res) ## I found no up and down-regulated genes
Therefore, could you please suggest as I am new to DESeq2 analysis and R? Thanks!
This is not really a DESeq2-related question since there is no technical problem. You can post it over at biostars.org if you want, adding the necessary details about the experimental design, the number of replicates etc, then people might be able to help. The simplest explanation(s) are probably that 1) there is indeed no effect of any of these factors or 2) your experiment is underpowered. As for 2) please indicate replicate numbers and some exploratory diagnostics such as a PCA.