Dataset Open Access

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

Alasoo, Kaur


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    <subfield code="a">&lt;p&gt;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 .&lt;/p&gt;

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

&lt;p&gt;#Extract differentially expressed genes in each condition&lt;br&gt;
ifng_genes = results(dds, contrast=c("condition_name","IFNg","naive")) &lt;br&gt;
sl1344_genes = results(dds, contrast=c("condition_name","SL1344","naive")) &lt;br&gt;
ifng_sl1344_genes = results(dds, contrast=c("condition_name","IFNg_SL1344","naive"))&lt;/p&gt;</subfield>
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