I have sent two sets (two batches in matter of sending for sequencing) of different samples (plasma) to small RNA-seq to Qiagen company
This is how my meta data look
> head(meta) batch group sex 30678.009 batch2 C Male 30678.010 batch2 C Female 30941.001 batch1 C Female 30941.002 batch1 C Male 30941.003 batch1 C Male 30941.004 batch1 C Male > tail(meta) batch group sex 30941.016 batch1 LT Female 30941.017 batch1 LT Male 30941.019 batch1 LT Male 30941.022 batch1 LT Female 30941.023 batch1 LT Male 30941.024 batch1 LT Female >
I want to extract differentially expressed RNAs between my two groups without batch effect
I am doing this
Is this correct please?
dds <- DESeqDataSetFromMatrix(countData = count, colData = meta, design= ~ batch + group) dds <- DESeq(dds, test="LRT", reduced=~batch) res <- results(dds) resultsNames(dds)  "Intercept" "batch_batch2_vs_batch1" "group_LT_vs_C" >