August 4, 2017 Dataset Open Access

Alasoo, Kaur

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    "description": "<p>We used likelihood ratio test implemented in DESeq2 v1.10.0 (test = \u201cLRT\u201d) 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:\u00a0http://www.biorxiv.org/content/early/2017/05/18/102392 .</p>\n\n<p>We used the following commands in DESeq2:<br>\n#Run DESeq2<br>\ndds = DESeq2::DESeqDataSetFromMatrix(combined_expression_data_filtered$counts, design, ~condition_name)\u00a0<br>\ndds = DESeq2::DESeq(dds, test = \"LRT\", reduced = ~ 1)</p>\n\n<p>#Extract differentially expressed genes in each condition<br>\nifng_genes = results(dds, contrast=c(\"condition_name\",\"IFNg\",\"naive\"))\u00a0<br>\nsl1344_genes = results(dds, contrast=c(\"condition_name\",\"SL1344\",\"naive\"))\u00a0<br>\nifng_sl1344_genes = results(dds, contrast=c(\"condition_name\",\"IFNg_SL1344\",\"naive\"))</p>", 
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    "title": "Differential gene expression in iPSC-derived macrophages after IFNg stimulation and Salmonella infection", 
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        "affiliation": "Wellcome Trust Sanger Institute", 
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