Sorry, sir pardon me I'm deleting this post due to put my own work in public platform. I get the result also in DESeq2 for Differential gene expression with this command but I can not define a class of sample in the script could anyone write the DESeq2 code? For reference, I want to say I have 9 samples 3 for each ( A1, A2, A3, B1, B2, B3, C1, C2, C3) I want to get differentially genes between A and C sample. Thanks!
dds <- DESeq(DESeq.md)
Edit by ATpoint (content ported from a duplicate question):
> resultsNames(dds)  "Intercept" "condition_LD_vs_CK" "condition_MD_vs_CK" > head(res) log2 fold change (MLE): condition MD vs CK Wald test p-value: condition MD vs CK DataFrame with 6 rows and 6 columns