For all analyses of datasets comparing data from the latest GeneLynx release (April 2004) and earlier with datasets from more recent Entrez Gene releases, mappings between GeneLynx and Entrez Gene identifiers were performed via EnsEMBL [40] gene and transcript intermediates.
Gene symbols for the 8.2 k unique genes were used as identifiers to perform GSEA.
Samples from both groups were stripped of identifiers before performing the tests for this study.
Finally, a simple linear regression of residuals from the median polish analysis on the cohort identifier is performed to quantify the cohort effects (Keyes and Li 2010).
Double-blinded, randomized clinical trial (ClinicalTrials.gov Identifier: NCT00982722) performed at Karolinska University Hospital, Sweden, April 2008 to November 2011.
Evaluation based on two different sets of nursing notes collected from a U.S. hospital suggests that, in terms of recall, the software out-performs a single human de-identifier (0.81) and performs at least as well as a consensus of two human de-identifiers (0.94).
This platform aims at unifying gene identifiers (ids) and performing gene set analysis.
Figure 3a shows how the reconstruction of a pseudonymized dataset using temporary identifiers can be performed with direct server-to-server communication.
These numbers could prove to be even higher if a more accurate probe match by sequence rather than gene identifiers would be performed, as has recently been shown [ 34].
All samples were obtained without identifiers from surgeries performed at the Brigham and Women's Hospital and at UCSF Medical Center and were fixed in formalin and assembled in a TMA.
