Information Technology Reference
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statistical analysis are usually applied to each input data set, filtering and
annotation steps are useful in most cases, but not mandatory in general (indi-
cated by the square brackets around the step descriptions in the figure). Note
that whereas usually one data loading and preprocessing step per workflow is
sucient, there may well be applications where more than one filtering, sta-
tistical analysis or annotation step is applied, and where then also different
results are obtained at different stages of the workflow.
6.2.1 Bioconductor Services
Having identified principal units of functionality for the analysis of microarray
data using Bioconductor packages, the following services (among others) were
provided for this application using the jETI technology (cf. Section 2.1.2):
•
AffyExpress filter1
applies a filter function to an ExpressionSet so that
at least a certain number of chips are greater than a given background
[350].
•
AffyExpress filter2
applies a filter function to an ExpressionSet so that
the range of a gene has to be greater than a given value (range) [350].
•
AffyExpress preprocess
performs preprocessing of Affymetrix microar-
ray data using the
pre.process
function of the AffyExpress package [350].
•
Annaffy aafTableAnn
creates a table given a set of probe IDs and desired
annotation types [286].
•
Annaffy aafTableInt
creates a table containing expression values given
an ExpressionSet. In the resulting HTML table, the expression values
will have backgrounds with varying intensities of green depending on the
expression measure [286].
•
CreateExpressionSet
creates an ExpressionSet object from expression
values and phenodata.
•
DifferentialExpressionAnalysis ReplicateArrays
performs a basic
differential expression analysis, suitable for a set of replicate arrays using
the limma package [290].
•
Expresso
performs preprocessing of Affymetrix GeneChip data [102].
Background correction, normalization, PM correction and summarization
methods are configurable.
•
GCRMA
performs preprocessing Affymetrix GeneChip data [351].
•
Genefilter CV
applies a filter function for the coecient of variation to
an ExpressionSet [104].
•
Genefilter kOverA
applies a filter function for k elements larger than A
to an ExpressionSet [104].
•
Genefilter maxA
applies filter function to filter according to the maxi-
mum to an ExpressionSet [104].
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