Similar protocols

Pipeline publication

[…] rn injury. As previously described (), the samples were divided into subcohorts of time since injury (e.g., 1–3 or 3–6 d post injury), and cases and controls were compared only within these subcohorts. ARDS cases were defined according to Berlin criteria, and controls were defined as non-ARDS mechanically ventilated patients. Criteria were assumed to apply to a patient if they were noted within ±1 day of the sample being drawn. Infection was defined in these cohorts as previously described (). Use of the Glue Grant was approved by both the Glue Grant Consortium and the Stanford University Institutional Review Board (protocol 29798)., Gene expression datasets that used Affymetrix arrays were gcRMA normalized using R package affy, and other arrays were quantile normalized using R package limma () if not already normalized. All microarray data were log-2 transformed, and probes were summarized to genes within datasets using a fixed-effect inverse variance model., Multicohort analysis of gene expression was done as previously described (–, ). Briefly, we applied two meta-analysis methods: one combining effect sizes using Hedges’ g, the other using Fisher’s sum-of-logs method combining p values. Genes set as “significant” passed a minimum false discovery rate (FDR) and a minimum effect size. We chose effect size thresholds that were relatively low so as to reduce false positives while still maintaining a high number of true positives ()., Gene ontology enrichment was tested usi […]

Pipeline specifications

Software tools GC–RMA, affy, limma