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All selected features are manually described in biological terms.
pRoloc provides the implementation for the phenoDisco novelty detection algorithm (Breckels et al., 2013) that, based on a minimal set of markers and unlabeled data, can be used to effectively detect new putative clusters in the data, beyond those that were initially manually described (Fig. 1).
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Whole mount RNA in situ hybridization was performed manually as described [41].
Spots of interest were excised manually as described previously [28] and subjected to mass spectrometric protein identification Proteins were identified by two approaches as described recently [29], [30].
The plates were then stained with crystal violet solution (Sigma Aldrich, St . Louis MO) and colonies were scored manually as described previously [35].
For IHC staining, TMA slides were processed and stained manually as described earlier [ 36].
All encoded globin sequences were aligned manually as described previously [ 42, 43].
Lesions were defined manually as described in Geva, Baron, Jones, Price, and Warburton (2012).
This initial alignment was refined manually (as described in Methods) to remove redundant sequences.
Adenomas were counted manually as described in the materials and methods section using a dissecting microscope.
Data from Genevestigator was normalized, quality controlled, and annotated manually as described previously [ 29].
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