Microarray Data Analysis Pipelines - User-Level Workflow Design: A Bioinformatics Perspective - page 131

Tabl e 6.1 Services in the microarray data analysis domain model

Service Input types Output types

AffyExpress Filter1 ExpressionSet ExpressionSet

AffyExpress Filter2 ExpressionSet ExpressionSet

AffymetrixCELData, ExpressionSet,
PhenoData

AffyExpress Preprocess

PdfFile, Plot

Annaffy AnnotationTable TopTable HtmlFile, Table

Annaffy ExpressionTable ExpressionSet HtmlFile, Table

ExpressionValues,

CreateExpressionSet ExpressionSet

PhenoData
DifferentialExpressionAnalysis- ExpressionSet TopTable,

4ReplicateArrays Table, Textfile

DilutionBenchmark-

ExpressionValues PdfFile, Plot

PreprocessingAssessment
Expresso AffymetrixCELData ExpressionValues

GCRMA AffymetrixCELData ExpressionValues

Genefilter CV ExpressionSet ExpressionSet

Genefilter kOverA ExpressionSet ExpressionSet

Genefilter maxA ExpressionSet ExpressionSet

Genefilter pOverA ExpressionSet ExpressionSet

GetPubMedAbstracts TopTable HtmlFile, Table

AffymetrixCELData,
PhenoData

LoadDilutionBenchmarkData -

LoadHgu133SpikeIn- AffymetrixCELData,

-

BenchmarkData PhenoData

AffymetrixCELData,
PhenoData

LoadSpikeInBenchmarkData -

ReadAffymetrixCELData - AffymetrixCELData

ReadPhenoData - PhenoData

RMA AffymetrixCELData ExpressionValues

SpikeInBenchmark-

ExpressionValues PdfFile, Plot

PreprocessingAssessment
SpikeInBenchmark-

ExpressionValues PdfFile, Plot

PreprocessingAssessment2
Threestep AffymetrixCELData ExpressionValues

WriteHtmlFile HtmlFile -

WritePdfFile PdfFile -

WriteTextFile TextFi l e -