I am currently performing a large RNA-seq analysis from mice PBMCs. The dataset contains around 6,000 transcriptomic profiles and I would like to use DESeq2 to identify the sets of differentially expressed genes in the different conditions. In total, I have 100 biological stimulations, and for each stimulation I have 30 control samples and 30 samples treated with a molecule of interests (so is have: (30 controls+30 treated) * 100 stimulations = 6,000 samples).
I want to identify, for each stimulation, the sets of differentially expressed genes between control samples and treated samples. I do not want to compare samples from the different stimulations. In total, I would like to have thus 100 lists of differentially expressed genes.
I have started to use deseq2 to identify these lists but deseq2 is spending lot of time to perform comparisons on which I am not interested with (comparisons between the biological stimulations).
For now, I have a table sampleTable which looks like that:
I am using DEseq2 using the following command:
DESeqDataSetFromHTSeqCount(sampleTable = sampleTable, directory = directory, design= ~ condition)
Could you please help me with that? How can I specify to deseq2 to not perform the comparisons between the biological stimulations, but rather between control and treated sample within each stimulation ?
Thank you and best,