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Last data update: 2014.03.03

R: Leukemia's microarray gene expression data (expressionSet).

leukemiasEset

R Documentation

Leukemia's microarray gene expression data (expressionSet).

Description

ExpressionSet containing gene expresion data from 60 bone marrow samples of patients with one of the four main types of leukemia (ALL, AML, CLL, CML) or no-leukemia controls.

Platform: Affymetrix Human Genome U133 Plus 2.0
Annotation: genemapperhgu133plus2 (CDF from GATExplorer)
Mapping: Gene Ensembl ID (20172 features)

Tissue: Bone Marrow
Cell type: Mononuclear cells isolated by Ficoll density centrifugation
Disease type:

Acute Lymphoblastic Leukemia (ALL). Subtype: c-ALL / pre-B-ALL without t(9;22)
Acute Myeloid Leukemia (AML). Subtype: Normal karyotype
Chronic Lymphocytic Leukemia (CLL)
Chronic Myeloid Leukemia (CML)
Non-leukemia and healthy bone marrow (NoL)

All samples were obtained from untreated patients at the time of diagnosis.

Preprocessing: The microarrays were normalized with RMA using a redefined probe mapping from Affymetrix probesets to Ensembl genes (Ensembl IDs ENSG). This alternative Chip Definition File (CDF) with complete unambiguous mapping of microarray probes to genes (GeneMapper) is available at GATExplorer (http://bioinfow.dep.usal.es/xgate/mapping/mapping.php) (Risueno et al. 2010).

Usage

data(leukemiasEset)

Format

ExpressionSet with phenoData:

Project: "Mile1" for all samples
Tissue: "BoneMarrow"
LeukemiaType: Leukemia type acronym: "ALL", "AML", "CLL", "CML" or "NoL"
LeukemiaTypeFullName: The full leukemia type name.
Subtype: "AML with normal karyotype and other abnormalities", or "c_ALL/Pre_B_ALL without t(9 22)" if applies

Details

Package:	leukemiasEset
Type:	Package
Version:	1.0
Date:	2013-03-13
License:	GPL (>=2)
LazyLoad:	yes

Author(s)

Author: Sara Aibar, Celia Fontanillo and Javier De Las Rivas. Bioinformatics and Functional Genomics Group. Cancer Research Center (CiC-IBMCC, CSIC/USAL). Salamanca. Spain.

Maintainer: Sara Aibar <saibar@usal.es>

Source

This is a subset of the samples collected by the Microarray Innovations in Leukemia (MILE) study (Kohlmann et al. 2008, Haferlach et al. 2010). Full study microarray raw data can be found at the NCBI Gene Expression Omnibus database (GEO, http://www.ncbi.nlm.nih.gov/geo/) under series accession number GSE13159. The selected samples are labelled keeping their source GEO IDs.

References

Kohlmann A, Kipps TJ, Rassenti LZ, Downing JR et al. An international standardization programme towards the application of gene expression profiling in routine leukaemia diagnostics: the Microarray Innovations in LEukemia study prephase. Br J Haematol (2008) 142(5):802-7. PMID: 18573112

Haferlach T, Kohlmann A, Wieczorek L, Basso G et al. Clinical utility of microarray-based gene expression profiling in the diagnosis and subclassification of leukemia: report from the International Microarray Innovations in Leukemia Study Group. J Clin Oncol (2010) 28(15):2529-37. PMID: 20406941

Risueno A, Fontanillo C, Dinger ME, De Las Rivas J. GATExplorer: genomic and transcriptomic explorer; mapping expression probes to gene loci, transcripts, exons and ncRNAs. BMC Bioinformatics (2010) 11:221. PMID: 20429936.

Examples

# Load expression set:
library(leukemiasEset)
data(leukemiasEset)

# ExpressionSet overview:
leukemiasEset

# Phenodata:
pData(leukemiasEset)

# Number of samples per class:
summary(leukemiasEset$LeukemiaType)

# For adding a prefix with the disease to the sample name:
sampleNames(leukemiasEset) <- paste(leukemiasEset$LeukemiaType, 
  sampleNames(leukemiasEset), sep="_")
colnames(exprs(leukemiasEset))

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(leukemiasEset)
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/leukemiasEset/leukemiasEset.Rd_%03d_medium.png", width=480, height=480)
> ### Name: leukemiasEset
> ### Title: Leukemia's microarray gene expression data (expressionSet).
> ### Aliases: leukemiasEset-package leukemiasEset
> ### Keywords: datasets expression microarrays cancer leukemia
> 
> ### ** Examples
> 
> # Load expression set:
> library(leukemiasEset)
> data(leukemiasEset)
> 
> # ExpressionSet overview:
> leukemiasEset
ExpressionSet (storageMode: lockedEnvironment)
assayData: 20172 features, 60 samples 
  element names: exprs, se.exprs 
protocolData
  sampleNames: GSM330151.CEL GSM330153.CEL ... GSM331677.CEL (60 total)
  varLabels: ScanDate
  varMetadata: labelDescription
phenoData
  sampleNames: GSM330151.CEL GSM330153.CEL ... GSM331677.CEL (60 total)
  varLabels: Project Tissue ... Subtype (5 total)
  varMetadata: labelDescription
featureData: none
experimentData: use 'experimentData(object)'
Annotation: genemapperhgu133plus2 
> 
> # Phenodata:
> pData(leukemiasEset)
              Project     Tissue LeukemiaType
GSM330151.CEL   Mile1 BoneMarrow          ALL
GSM330153.CEL   Mile1 BoneMarrow          ALL
GSM330154.CEL   Mile1 BoneMarrow          ALL
GSM330157.CEL   Mile1 BoneMarrow          ALL
GSM330171.CEL   Mile1 BoneMarrow          ALL
GSM330174.CEL   Mile1 BoneMarrow          ALL
GSM330178.CEL   Mile1 BoneMarrow          ALL
GSM330182.CEL   Mile1 BoneMarrow          ALL
GSM330185.CEL   Mile1 BoneMarrow          ALL
GSM330186.CEL   Mile1 BoneMarrow          ALL
GSM330195.CEL   Mile1 BoneMarrow          ALL
GSM330201.CEL   Mile1 BoneMarrow          ALL
GSM330532.CEL   Mile1 BoneMarrow          AML
GSM330546.CEL   Mile1 BoneMarrow          AML
GSM330559.CEL   Mile1 BoneMarrow          AML
GSM330566.CEL   Mile1 BoneMarrow          AML
GSM330571.CEL   Mile1 BoneMarrow          AML
GSM330574.CEL   Mile1 BoneMarrow          AML
GSM330580.CEL   Mile1 BoneMarrow          AML
GSM330584.CEL   Mile1 BoneMarrow          AML
GSM330593.CEL   Mile1 BoneMarrow          AML
GSM330603.CEL   Mile1 BoneMarrow          AML
GSM330611.CEL   Mile1 BoneMarrow          AML
GSM330612.CEL   Mile1 BoneMarrow          AML
GSM330933.CEL   Mile1 BoneMarrow          CLL
GSM330934.CEL   Mile1 BoneMarrow          CLL
GSM330969.CEL   Mile1 BoneMarrow          CLL
GSM330979.CEL   Mile1 BoneMarrow          CLL
GSM330980.CEL   Mile1 BoneMarrow          CLL
GSM330982.CEL   Mile1 BoneMarrow          CLL
GSM330987.CEL   Mile1 BoneMarrow          CLL
GSM330999.CEL   Mile1 BoneMarrow          CLL
GSM331004.CEL   Mile1 BoneMarrow          CLL
GSM331009.CEL   Mile1 BoneMarrow          CLL
GSM331037.CEL   Mile1 BoneMarrow          CLL
GSM331048.CEL   Mile1 BoneMarrow          CLL
GSM331377.CEL   Mile1 BoneMarrow          CML
GSM331378.CEL   Mile1 BoneMarrow          CML
GSM331381.CEL   Mile1 BoneMarrow          CML
GSM331382.CEL   Mile1 BoneMarrow          CML
GSM331383.CEL   Mile1 BoneMarrow          CML
GSM331386.CEL   Mile1 BoneMarrow          CML
GSM331387.CEL   Mile1 BoneMarrow          CML
GSM331388.CEL   Mile1 BoneMarrow          CML
GSM331389.CEL   Mile1 BoneMarrow          CML
GSM331390.CEL   Mile1 BoneMarrow          CML
GSM331392.CEL   Mile1 BoneMarrow          CML
GSM331393.CEL   Mile1 BoneMarrow          CML
GSM331660.CEL   Mile1 BoneMarrow          NoL
GSM331661.CEL   Mile1 BoneMarrow          NoL
GSM331663.CEL   Mile1 BoneMarrow          NoL
GSM331666.CEL   Mile1 BoneMarrow          NoL
GSM331668.CEL   Mile1 BoneMarrow          NoL
GSM331670.CEL   Mile1 BoneMarrow          NoL
GSM331671.CEL   Mile1 BoneMarrow          NoL
GSM331672.CEL   Mile1 BoneMarrow          NoL
GSM331673.CEL   Mile1 BoneMarrow          NoL
GSM331674.CEL   Mile1 BoneMarrow          NoL
GSM331675.CEL   Mile1 BoneMarrow          NoL
GSM331677.CEL   Mile1 BoneMarrow          NoL
                              LeukemiaTypeFullName
GSM330151.CEL         Acute Lymphoblastic Leukemia
GSM330153.CEL         Acute Lymphoblastic Leukemia
GSM330154.CEL         Acute Lymphoblastic Leukemia
GSM330157.CEL         Acute Lymphoblastic Leukemia
GSM330171.CEL         Acute Lymphoblastic Leukemia
GSM330174.CEL         Acute Lymphoblastic Leukemia
GSM330178.CEL         Acute Lymphoblastic Leukemia
GSM330182.CEL         Acute Lymphoblastic Leukemia
GSM330185.CEL         Acute Lymphoblastic Leukemia
GSM330186.CEL         Acute Lymphoblastic Leukemia
GSM330195.CEL         Acute Lymphoblastic Leukemia
GSM330201.CEL         Acute Lymphoblastic Leukemia
GSM330532.CEL           Acute Myelogenous Leukemia
GSM330546.CEL           Acute Myelogenous Leukemia
GSM330559.CEL           Acute Myelogenous Leukemia
GSM330566.CEL           Acute Myelogenous Leukemia
GSM330571.CEL           Acute Myelogenous Leukemia
GSM330574.CEL           Acute Myelogenous Leukemia
GSM330580.CEL           Acute Myelogenous Leukemia
GSM330584.CEL           Acute Myelogenous Leukemia
GSM330593.CEL           Acute Myelogenous Leukemia
GSM330603.CEL           Acute Myelogenous Leukemia
GSM330611.CEL           Acute Myelogenous Leukemia
GSM330612.CEL           Acute Myelogenous Leukemia
GSM330933.CEL         Chronic Lymphocytic Leukemia
GSM330934.CEL         Chronic Lymphocytic Leukemia
GSM330969.CEL         Chronic Lymphocytic Leukemia
GSM330979.CEL         Chronic Lymphocytic Leukemia
GSM330980.CEL         Chronic Lymphocytic Leukemia
GSM330982.CEL         Chronic Lymphocytic Leukemia
GSM330987.CEL         Chronic Lymphocytic Leukemia
GSM330999.CEL         Chronic Lymphocytic Leukemia
GSM331004.CEL         Chronic Lymphocytic Leukemia
GSM331009.CEL         Chronic Lymphocytic Leukemia
GSM331037.CEL         Chronic Lymphocytic Leukemia
GSM331048.CEL         Chronic Lymphocytic Leukemia
GSM331377.CEL         Chronic Myelogenous Leukemia
GSM331378.CEL         Chronic Myelogenous Leukemia
GSM331381.CEL         Chronic Myelogenous Leukemia
GSM331382.CEL         Chronic Myelogenous Leukemia
GSM331383.CEL         Chronic Myelogenous Leukemia
GSM331386.CEL         Chronic Myelogenous Leukemia
GSM331387.CEL         Chronic Myelogenous Leukemia
GSM331388.CEL         Chronic Myelogenous Leukemia
GSM331389.CEL         Chronic Myelogenous Leukemia
GSM331390.CEL         Chronic Myelogenous Leukemia
GSM331392.CEL         Chronic Myelogenous Leukemia
GSM331393.CEL         Chronic Myelogenous Leukemia
GSM331660.CEL Non-leukemia and healthy bone marrow
GSM331661.CEL Non-leukemia and healthy bone marrow
GSM331663.CEL Non-leukemia and healthy bone marrow
GSM331666.CEL Non-leukemia and healthy bone marrow
GSM331668.CEL Non-leukemia and healthy bone marrow
GSM331670.CEL Non-leukemia and healthy bone marrow
GSM331671.CEL Non-leukemia and healthy bone marrow
GSM331672.CEL Non-leukemia and healthy bone marrow
GSM331673.CEL Non-leukemia and healthy bone marrow
GSM331674.CEL Non-leukemia and healthy bone marrow
GSM331675.CEL Non-leukemia and healthy bone marrow
GSM331677.CEL Non-leukemia and healthy bone marrow
                                                        Subtype
GSM330151.CEL                   c_ALL/Pre_B_ALL without t(9 22)
GSM330153.CEL                   c_ALL/Pre_B_ALL without t(9 22)
GSM330154.CEL                   c_ALL/Pre_B_ALL without t(9 22)
GSM330157.CEL                   c_ALL/Pre_B_ALL without t(9 22)
GSM330171.CEL                   c_ALL/Pre_B_ALL without t(9 22)
GSM330174.CEL                   c_ALL/Pre_B_ALL without t(9 22)
GSM330178.CEL                   c_ALL/Pre_B_ALL without t(9 22)
GSM330182.CEL                   c_ALL/Pre_B_ALL without t(9 22)
GSM330185.CEL                   c_ALL/Pre_B_ALL without t(9 22)
GSM330186.CEL                   c_ALL/Pre_B_ALL without t(9 22)
GSM330195.CEL                   c_ALL/Pre_B_ALL without t(9 22)
GSM330201.CEL                   c_ALL/Pre_B_ALL without t(9 22)
GSM330532.CEL AML with normal karyotype and other abnormalities
GSM330546.CEL AML with normal karyotype and other abnormalities
GSM330559.CEL AML with normal karyotype and other abnormalities
GSM330566.CEL AML with normal karyotype and other abnormalities
GSM330571.CEL AML with normal karyotype and other abnormalities
GSM330574.CEL AML with normal karyotype and other abnormalities
GSM330580.CEL AML with normal karyotype and other abnormalities
GSM330584.CEL AML with normal karyotype and other abnormalities
GSM330593.CEL AML with normal karyotype and other abnormalities
GSM330603.CEL AML with normal karyotype and other abnormalities
GSM330611.CEL AML with normal karyotype and other abnormalities
GSM330612.CEL AML with normal karyotype and other abnormalities
GSM330933.CEL                                                  
GSM330934.CEL                                                  
GSM330969.CEL                                                  
GSM330979.CEL                                                  
GSM330980.CEL                                                  
GSM330982.CEL                                                  
GSM330987.CEL                                                  
GSM330999.CEL                                                  
GSM331004.CEL                                                  
GSM331009.CEL                                                  
GSM331037.CEL                                                  
GSM331048.CEL                                                  
GSM331377.CEL                                                  
GSM331378.CEL                                                  
GSM331381.CEL                                                  
GSM331382.CEL                                                  
GSM331383.CEL                                                  
GSM331386.CEL                                                  
GSM331387.CEL                                                  
GSM331388.CEL                                                  
GSM331389.CEL                                                  
GSM331390.CEL                                                  
GSM331392.CEL                                                  
GSM331393.CEL                                                  
GSM331660.CEL                                                  
GSM331661.CEL                                                  
GSM331663.CEL                                                  
GSM331666.CEL                                                  
GSM331668.CEL                                                  
GSM331670.CEL                                                  
GSM331671.CEL                                                  
GSM331672.CEL                                                  
GSM331673.CEL                                                  
GSM331674.CEL                                                  
GSM331675.CEL                                                  
GSM331677.CEL                                                  
> 
> # Number of samples per class:
> summary(leukemiasEset$LeukemiaType)
ALL AML CLL CML NoL 
 12  12  12  12  12 
> 
> # For adding a prefix with the disease to the sample name:
> sampleNames(leukemiasEset) <- paste(leukemiasEset$LeukemiaType, 
+   sampleNames(leukemiasEset), sep="_")
> colnames(exprs(leukemiasEset))
 [1] "ALL_GSM330151.CEL" "ALL_GSM330153.CEL" "ALL_GSM330154.CEL"
 [4] "ALL_GSM330157.CEL" "ALL_GSM330171.CEL" "ALL_GSM330174.CEL"
 [7] "ALL_GSM330178.CEL" "ALL_GSM330182.CEL" "ALL_GSM330185.CEL"
[10] "ALL_GSM330186.CEL" "ALL_GSM330195.CEL" "ALL_GSM330201.CEL"
[13] "AML_GSM330532.CEL" "AML_GSM330546.CEL" "AML_GSM330559.CEL"
[16] "AML_GSM330566.CEL" "AML_GSM330571.CEL" "AML_GSM330574.CEL"
[19] "AML_GSM330580.CEL" "AML_GSM330584.CEL" "AML_GSM330593.CEL"
[22] "AML_GSM330603.CEL" "AML_GSM330611.CEL" "AML_GSM330612.CEL"
[25] "CLL_GSM330933.CEL" "CLL_GSM330934.CEL" "CLL_GSM330969.CEL"
[28] "CLL_GSM330979.CEL" "CLL_GSM330980.CEL" "CLL_GSM330982.CEL"
[31] "CLL_GSM330987.CEL" "CLL_GSM330999.CEL" "CLL_GSM331004.CEL"
[34] "CLL_GSM331009.CEL" "CLL_GSM331037.CEL" "CLL_GSM331048.CEL"
[37] "CML_GSM331377.CEL" "CML_GSM331378.CEL" "CML_GSM331381.CEL"
[40] "CML_GSM331382.CEL" "CML_GSM331383.CEL" "CML_GSM331386.CEL"
[43] "CML_GSM331387.CEL" "CML_GSM331388.CEL" "CML_GSM331389.CEL"
[46] "CML_GSM331390.CEL" "CML_GSM331392.CEL" "CML_GSM331393.CEL"
[49] "NoL_GSM331660.CEL" "NoL_GSM331661.CEL" "NoL_GSM331663.CEL"
[52] "NoL_GSM331666.CEL" "NoL_GSM331668.CEL" "NoL_GSM331670.CEL"
[55] "NoL_GSM331671.CEL" "NoL_GSM331672.CEL" "NoL_GSM331673.CEL"
[58] "NoL_GSM331674.CEL" "NoL_GSM331675.CEL" "NoL_GSM331677.CEL"
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>