Differential gene expression in iPSC-derived macrophages after IFNg stimulation and Salmonella infection

We used likelihood ratio test implemented in DESeq2 v1.10.0 (test = “LRT”) to test if a model that allowed different mean expression in each condition explained the data better than a null model assuming the same mean expression across conditions. See the manuscript for more details: http://www.biorxiv.org/content/early/2017/05/18/102392 .

We used the following commands in DESeq2:
#Run DESeq2
dds = DESeq2::DESeqDataSetFromMatrix(combined_expression_data_filtered$counts, design, ~condition_name) 
dds = DESeq2::DESeq(dds, test = "LRT", reduced = ~ 1)

#Extract differentially expressed genes in each condition
ifng_genes = results(dds, contrast=c("condition_name","IFNg","naive")) 
sl1344_genes = results(dds, contrast=c("condition_name","SL1344","naive")) 
ifng_sl1344_genes = results(dds, contrast=c("condition_name","IFNg_SL1344","naive"))