\name{pwLines} \Rdversion{1.1} \alias{pwLines} \docType{data} \title{ A representation of Bild's HMEC lines for pathway signature identification } \description{ A representation of Bild's HMEC lines for pathway signature identification %% ~~ A concise (1-5 lines) description of the dataset. ~~ } \usage{data(pwLines)} \format{ The format is: Formal class 'ExpressionSet' [package "Biobase"] with 6 slots ..@ assayData : ..@ phenoData :Formal class 'AnnotatedDataFrame' [package "Biobase"] with 4 slots .. .. ..@ varMetadata :'data.frame': 28 obs. of 1 variable: .. .. .. ..$ labelDescription: chr [1:28] NA NA NA NA ... .. .. ..@ data :'data.frame': 55 obs. of 28 variables: .. .. .. ..$ gsmid : chr [1:55] "GSM70597" "GSM70598" "GSM70599" "GSM70600" ... .. .. .. ..$ gsmlabel : Factor w/ 55 levels "BCAT-8","BCAT-9",..: 19 21 22 23 24 25 26 27 28 20 ... .. .. .. ..$ perturb : chr [1:55] "GFP" "GFP" "GFP" "GFP" ... .. .. .. ..$ title : Factor w/ 55 levels "BCAT-8","BCAT-9",..: 19 21 22 23 24 25 26 27 28 20 ... .. .. .. .. ..- attr(*, "names")= chr [1:55] "V2" "V3" "V4" "V5" ... .. .. .. ..$ geo_accession : Factor w/ 55 levels "GSM70597","GSM70598",..: 1 2 3 4 5 6 7 8 9 10 ... .. .. .. .. ..- attr(*, "names")= chr [1:55] "V2" "V3" "V4" "V5" ... .. .. .. ..$ status : Factor w/ 1 level "Public on Nov 07 2005": 1 1 1 1 1 1 1 1 1 1 ... .. .. .. .. ..- attr(*, "names")= chr [1:55] "V2" "V3" "V4" "V5" ... .. .. .. ..$ submission_date : Factor w/ 1 level "Aug 17 2005": 1 1 1 1 1 1 1 1 1 1 ... .. .. .. .. ..- attr(*, "names")= chr [1:55] "V2" "V3" "V4" "V5" ... .. .. .. ..$ last_update_date : Factor w/ 1 level "Nov 07 2005": 1 1 1 1 1 1 1 1 1 1 ... .. .. .. .. ..- attr(*, "names")= chr [1:55] "V2" "V3" "V4" "V5" ... .. .. .. ..$ type : Factor w/ 1 level "RNA": 1 1 1 1 1 1 1 1 1 1 ... .. .. .. .. ..- attr(*, "names")= chr [1:55] "V2" "V3" "V4" "V5" ... .. .. .. ..$ channel_count : Factor w/ 1 level "1": 1 1 1 1 1 1 1 1 1 1 ... .. .. .. .. ..- attr(*, "names")= chr [1:55] "V2" "V3" "V4" "V5" ... .. .. .. ..$ source_name_ch1 : Factor w/ 1 level "mammary epithelial cells expressing oncogenes (or GFP control)": 1 1 1 1 1 1 1 1 1 1 ... .. .. .. .. ..- attr(*, "names")= chr [1:55] "V2" "V3" "V4" "V5" ... .. .. .. ..$ organism_ch1 : Factor w/ 1 level "Homo sapiens": 1 1 1 1 1 1 1 1 1 1 ... .. .. .. .. ..- attr(*, "names")= chr [1:55] "V2" "V3" "V4" "V5" ... .. .. .. ..$ characteristics_ch1 : Factor w/ 1 level "mammary epithelial cells expressing oncogenes (or GFP control)": 1 1 1 1 1 1 1 1 1 1 ... .. .. .. .. ..- attr(*, "names")= chr [1:55] "V2" "V3" "V4" "V5" ... .. .. .. ..$ molecule_ch1 : Factor w/ 1 level "total RNA": 1 1 1 1 1 1 1 1 1 1 ... .. .. .. .. ..- attr(*, "names")= chr [1:55] "V2" "V3" "V4" "V5" ... .. .. .. ..$ label_ch1 : Factor w/ 1 level "biotin": 1 1 1 1 1 1 1 1 1 1 ... .. .. .. .. ..- attr(*, "names")= chr [1:55] "V2" "V3" "V4" "V5" ... .. .. .. ..$ description : Factor w/ 1 level "RNA was extracted from human mammary epithelial cells expressing oncogenes (or GFP control)": 1 1 1 1 1 1 1 1 1 1 ... .. .. .. .. ..- attr(*, "names")= chr [1:55] "V2" "V3" "V4" "V5" ... .. .. .. ..$ data_processing : Factor w/ 1 level "Affymetrix Microarray Suite version 5.0": 1 1 1 1 1 1 1 1 1 1 ... .. .. .. .. ..- attr(*, "names")= chr [1:55] "V2" "V3" "V4" "V5" ... .. .. .. ..$ platform_id : Factor w/ 1 level "GPL570": 1 1 1 1 1 1 1 1 1 1 ... .. .. .. .. ..- attr(*, "names")= chr [1:55] "V2" "V3" "V4" "V5" ... .. .. .. ..$ contact_name : Factor w/ 1 level "Joseph,R.,Nevins": 1 1 1 1 1 1 1 1 1 1 ... .. .. .. .. ..- attr(*, "names")= chr [1:55] "V2" "V3" "V4" "V5" ... .. .. .. ..$ contact_department : Factor w/ 1 level "IGSP": 1 1 1 1 1 1 1 1 1 1 ... .. .. .. .. ..- attr(*, "names")= chr [1:55] "V2" "V3" "V4" "V5" ... .. .. .. ..$ contact_institute : Factor w/ 1 level "Duke University": 1 1 1 1 1 1 1 1 1 1 ... .. .. .. .. ..- attr(*, "names")= chr [1:55] "V2" "V3" "V4" "V5" ... .. .. .. ..$ contact_address : Factor w/ 1 level "2133 CIEMAS, 101 Science Dr.": 1 1 1 1 1 1 1 1 1 1 ... .. .. .. .. ..- attr(*, "names")= chr [1:55] "V2" "V3" "V4" "V5" ... .. .. .. ..$ contact_city : Factor w/ 1 level "Durham": 1 1 1 1 1 1 1 1 1 1 ... .. .. .. .. ..- attr(*, "names")= chr [1:55] "V2" "V3" "V4" "V5" ... .. .. .. ..$ contact_state : Factor w/ 1 level "NC": 1 1 1 1 1 1 1 1 1 1 ... .. .. .. .. ..- attr(*, "names")= chr [1:55] "V2" "V3" "V4" "V5" ... .. .. .. ..$ contact_zip/postal_code: Factor w/ 1 level "27708": 1 1 1 1 1 1 1 1 1 1 ... .. .. .. .. ..- attr(*, "names")= chr [1:55] "V2" "V3" "V4" "V5" ... .. .. .. ..$ contact_country : Factor w/ 1 level "USA": 1 1 1 1 1 1 1 1 1 1 ... .. .. .. .. ..- attr(*, "names")= chr [1:55] "V2" "V3" "V4" "V5" ... .. .. .. ..$ supplementary_file : Factor w/ 1 level "NONE": 1 1 1 1 1 1 1 1 1 1 ... .. .. .. .. ..- attr(*, "names")= chr [1:55] "V2" "V3" "V4" "V5" ... .. .. .. ..$ data_row_count : Factor w/ 1 level "54675": 1 1 1 1 1 1 1 1 1 1 ... .. .. .. .. ..- attr(*, "names")= chr [1:55] "V2" "V3" "V4" "V5" ... .. .. ..@ 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': 54675 obs. of 16 variables: .. .. .. ..$ ID : Factor w/ 54676 levels "1007_s_at","1053_at",..: 1 2 3 4 5 6 7 8 9 10 ... .. .. .. ..$ GB_ACC : Factor w/ 51277 levels "AF276507","AK074161",..: 82 21 83 85 17 16 84 87 19 15 ... .. .. .. ..$ SPOT_ID : chr [1:54675] 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 "Mar 11, 2009",..: 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/ 51843 levels "J02843 /FEATURE=cds /DEFINITION=HUMCYPIIE Human cytochrome P450IIE1 (ethanol-inducible) gene, complete cds",..: 8 7 9 11 3 2 10 13 5 1 ... .. .. .. ..$ Representative.Public.ID : Factor w/ 51339 levels "AF276507","AK074161",..: 82 21 83 85 17 16 84 87 19 15 ... .. .. .. ..$ Gene.Title : Factor w/ 23061 levels "ADAM metallopeptidase domain 32",..: 34 59 42 54 41 76 72 58 19 33 ... .. .. .. ..$ Gene.Symbol : Factor w/ 20828 levels "ADAM32","AFG3L1",..: 26 59 40 50 38 75 68 54 18 25 ... .. .. .. ..$ ENTREZ_GENE_ID : Factor w/ 20828 levels "10406","11078",..: 63 59 51 64 48 62 61 3 60 24 ... .. .. .. ..$ RefSeq.Transcript.ID : Factor w/ 20082 levels "","NM_000409",..: 17 22 19 26 2 25 24 32 23 4 ... .. .. .. ..$ Gene.Ontology.Biological.Process: Factor w/ 8891 levels "","0000122 // negative regulation of transcription from RNA polymerase II promoter // inferred from electronic annotation /// 0006"| __truncated__,..: 20 11 36 8 39 18 5 23 35 49 ... .. .. .. ..$ Gene.Ontology.Cellular.Component: Factor w/ 6677 levels "","0000151 // ubiquitin ligase complex // inferred from electronic annotation /// 0005634 // nucleus // inferred from electronic a"| __truncated__,..: 43 21 1 20 44 1 18 28 8 36 ... .. .. .. ..$ Gene.Ontology.Molecular.Function: Factor w/ 8929 levels "","0000166 // nucleotide binding // inferred from electronic annotation /// 0001784 // phosphotyrosine binding // inferred from el"| __truncated__,..: 9 5 10 23 47 7 22 38 41 37 ... .. .. ..@ 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 "hgu133plus2.db" ..@ .__classVersion__:Formal class 'Versions' [package "Biobase"] with 1 slots .. .. ..@ .Data:List of 4 .. .. .. ..$ : int [1:3] 2 10 0 .. .. .. ..$ : int [1:3] 2 3 11 .. .. .. ..$ : int [1:3] 1 1 0 .. .. .. ..$ : int [1:3] 1 0 0 } \details{ %% ~~ If necessary, more details than the __description__ above ~~ } \source{ %% ~~ reference to a publication or URL from which the data were obtained ~~ } \references{ %% ~~ possibly secondary sources and usages ~~ } \examples{ data(pwLines) ## maybe str(pwLines) ; plot(pwLines) ... } \keyword{datasets}