dunkley2006 | R Documentation |
This is the data from Dunkley et al., Mapping the Arabidopsis organelle proteome, PNAS 2006 (PMID 16618929). See below for more details.
data(dunkley2006)
data(dunkley2006goCC)
The data is an instance of class MSnSet
from package MSnbase
.
This is a LOPIT experiment. Normalised intensities for 689 proteins
for four iTRAQ 4-plex labelled fraction and 2 membrane preparation in
duplicate (16 samples, see phenoData(dunkley2006)
for more
details) are provided.
Partial least square discriminant analysis (PLSDA) has originally been
applied to the test data fData(dunkley)$markers)
; assignment results are
available with fData(dunkley)$assigned)
for 5 organelles.
This dataset was also used in testing the phenotype discovery algorithm from
Breckels et al., The Effect of Organelle Discovery upon Sub-Cellular
Protein Localisation, J Proteomics, In Press., see phenoDisco
.
New phenotype clusters identified from algorithm application are available as
pd.2013
feature meta-data.
The dunkley2006goCC
instance contains binary assay data. Its
columns represent GO CC terms that have been observed for the object's
features. A 1 indicates that a GO term has been associated to a given
feature (protein); a 0 means not such association was found in the GO
ontology.
Supporting Information on http://www.pnas.org/content/103/17/6518.abstract.
Dunkley TP, Hester S, Shadforth IP, Runions J, Weimar T, Hanton SL, Griffin JL, Bessant C, Brandizzi F, Hawes C, Watson RB, Dupree P, Lilley KS. Mapping the Arabidopsis organelle proteome. Proc Natl Acad Sci U S A. 2006 Apr 25;103(17):6518-23. Epub 2006 Apr 17. PubMed PMID: 16618929; PubMed Central PMCID: PMC1458916.
Breckels LM, Gatto L, Christoforou A, Groen AJ, Lilley KS and Trotter MWB. The Effect of Organelle Discovery upon Sub-Cellular Protein Localisation J Proteomics. In Press.
data(dunkley2006)
dunkley2006
phenoData(dunkley2006)
## Input training data (organelle markers)
table(fData(dunkley2006)$markers)
## PLSDA assignment results
table(fData(dunkley2006)$assigned)
## PhenoDisco results
table(fData(dunkley2006)$pd.2013)
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