eset {phenoTest} | R Documentation

## Example data.

### Description

Example data of class ExpressionSet.

### Usage

    data(eset)

### Format

The format is: Formal class 'ExpressionSet' [package "Biobase"] with 7 slots ..@ assayData :<environment: 0x1050d9390> ..@ phenoData :Formal class 'AnnotatedDataFrame' [package "Biobase"] with 4 slots .. .. ..@ varMetadata :'data.frame': 7 obs. of 1 variable: .. .. .. ..$ labelDescription: chr [1:7] NA NA NA NA ... .. .. ..@ data :'data.frame': 286 obs. of 7 variables: .. .. .. ..$ PID : int [1:286] 3 5 6 7 8 9 11 14 15 17 ... .. .. .. ..$ GEOaccession : Factor w/ 286 levels "GSM36777","GSM36778",..: 17 20 21 22 24 25 58 59 60 61 ... .. .. .. ..$ lymph.node.status: chr [1:286] "negative" "negative" "negative" "negative" ... .. .. .. ..$ Months2Relapse : int [1:286] 101 118 9 106 37 125 109 14 99 137 ... .. .. .. ..$ Relapse : int [1:286] 0 0 1 0 1 0 0 1 0 0 ... .. .. .. ..$ ER.Status : num [1:286] 0 1 0 0 0 1 1 0 1 1 ... .. .. .. ..$ BrainRelapse : int [1:286] 0 0 0 0 0 0 0 0 0 0 ... .. .. ..@ dimLabels : chr [1:2] "sampleNames" "sampleColumns" .. .. ..@ .__classVersion__:Formal class 'Versions' [package "Biobase"] with 1 slots .. .. .. .. ..@ .Data:List of 1 .. .. .. .. .. ..$ : int [1:3] 1 1 0 ..@ featureData :Formal class 'AnnotatedDataFrame' [package "Biobase"] with 4 slots .. .. ..@ varMetadata :'data.frame': 16 obs. of 3 variables: .. .. .. ..$ Column : chr [1:16] "ID" "GB_ACC" "SPOT_ID" "Species Scientific Name" ... .. .. .. ..$ Description : Factor w/ 15 levels "","A gene symbol, when one is available (from UniGene).",..: 3 5 15 13 12 1 11 1 10 14 ... .. .. .. ..$ labelDescription: chr [1:16] NA NA NA NA ... .. .. ..@ data :'data.frame': 1000 obs. of 16 variables: .. .. .. ..$ ID : Factor w/ 22284 levels "1007_s_at","1053_at",..: 1 2 3 4 5 6 7 8 9 10 ... .. .. .. ..$ GB_ACC : Factor w/ 21129 levels "AF052179","AF061832",..: 93 30 95 97 25 24 96 99 28 20 ... .. .. .. ..$ SPOT_ID : chr [1:1000] NA NA NA NA ... .. .. .. ..$ Species.Scientific.Name : Factor w/ 2 levels "Homo sapiens",..: 1 1 1 1 1 1 1 1 1 1 ... .. .. .. ..$ Annotation.Date : Factor w/ 2 levels "Jul 11, 2007",..: 1 1 1 1 1 1 1 1 1 1 ... .. .. .. ..$ Sequence.Type : Factor w/ 4 levels "Consensus sequence",..: 2 2 2 2 2 2 2 2 2 2 ... .. .. .. ..$ Sequence.Source : Factor w/ 3 levels "Affymetrix Proprietary Database",..: 1 2 1 2 1 2 1 1 2 1 ... .. .. .. ..$ Target.Description : Factor w/ 21363 levels "Consensus includes gb:AI656011 /FEA=EST /DB_XREF=gi:4739990 /DB_XREF=est:tt42e08.x1 /CLONE=IMAGE:2243462 /UG=Hs.116875 KIAA0156"| __truncated__,..: 16 13 18 20 8 7 19 22 11 4 ... .. .. .. ..$ Representative.Public.ID : Factor w/ 21197 levels "AF052179","AF061832",..: 93 30 95 97 25 24 96 99 28 20 ... .. .. .. ..$ Gene.Title : Factor w/ 14208 levels "ADP-ribosylation factor 1",..: 35 66 46 60 44 97 96 64 26 33 ... .. .. .. ..$ Gene.Symbol : Factor w/ 13293 levels "ABCF1","ARF1",..: 20 59 40 53 33 96 94 58 15 18 ... .. .. .. ..$ ENTREZ_GENE_ID : chr [1:1000] "780" "5982" "3310" "7849" ... .. .. .. ..$ RefSeq.Transcript.ID : Factor w/ 13074 levels "NM_000409","NM_000661 /// NM_001024921",..: 37 45 41 52 1 50 49 82 47 4 ... .. .. .. ..$ Gene.Ontology.Biological.Process: Factor w/ 7245 levels "","0000074 // regulation of progression through cell cycle // traceable author statement /// 0006139 // nucleobase, nucleoside, nu"| __truncated__,..: 61 22 78 32 79 60 14 63 72 20 ... .. .. .. ..$ Gene.Ontology.Cellular.Component: Factor w/ 4148 levels "","0000502 // proteasome complex (sensu Eukaryota) // traceable author statement /// 0005634 // nucleus // inferred from electroni"| __truncated__,..: 72 45 1 44 1 1 42 71 6 68 ... .. .. .. ..$ Gene.Ontology.Molecular.Function: Factor w/ 7314 levels "","0000049 // tRNA binding // non-traceable author statement /// 0000166 // nucleotide binding // inferred from electronic annotat"| __truncated__,..: 23 26 27 40 81 18 39 71 74 69 ... .. .. ..@ dimLabels : chr [1:2] "featureNames" "featureColumns" .. .. ..@ .__classVersion__:Formal class 'Versions' [package "Biobase"] with 1 slots .. .. .. .. ..@ .Data:List of 1 .. .. .. .. .. ..$ : int [1:3] 1 1 0 ..@ experimentData :Formal class 'MIAME' [package "Biobase"] with 13 slots .. .. ..@ name : chr "" .. .. ..@ lab : chr "" .. .. ..@ contact : chr "" .. .. ..@ title : chr "" .. .. ..@ abstract : chr "" .. .. ..@ url : chr "" .. .. ..@ pubMedIds : chr "" .. .. ..@ samples : list() .. .. ..@ hybridizations : list() .. .. ..@ normControls : list() .. .. ..@ preprocessing : list() .. .. ..@ other : list() .. .. ..@ .__classVersion__:Formal class 'Versions' [package "Biobase"] with 1 slots .. .. .. .. ..@ .Data:List of 1 .. .. .. .. .. ..$ : int [1:3] 1 0 0 ..@ annotation : chr "hgu133a" ..@ protocolData :Formal class 'AnnotatedDataFrame' [package "Biobase"] with 4 slots .. .. ..@ varMetadata :'data.frame': 0 obs. of 1 variable: .. .. .. ..$ labelDescription: chr(0) .. .. ..@ data :'data.frame': 286 obs. of 0 variables .. .. ..@ dimLabels : chr [1:2] "sampleNames" "sampleColumns" .. .. ..@ .__classVersion__:Formal class 'Versions' [package "Biobase"] with 1 slots .. .. .. .. ..@ .Data:List of 1 .. .. .. .. .. ..$ : int [1:3] 1 1 0 ..@ .__classVersion__:Formal class 'Versions' [package "Biobase"] with 1 slots .. .. ..@ .Data:List of 4 .. .. .. ..$ : int [1:3] 2 12 0 .. .. .. ..$ : int [1:3] 2 10 0 .. .. .. ..$ : int [1:3] 1 3 0 .. .. .. ..$ : int [1:3] 1 0 0

### References

Has been obtained from GEO (GSE2034). Only first 1000 probesets where stored (the rest has been removed).

### Examples

    data(eset)
    ## maybe str(eset) ; plot(eset) ...

[Package phenoTest version 1.34.0 Index]