Transcriptome dataset for Chronic Lymphocytic Leukemia patients from Chuang et al. (2012)


This dataset involves 130 patients with chronic lymphocytic leukemia (CLL). When enrolled in the study, these CLL patients had not received prior therapy for CLL. Additional covariate about the time to treatment (i.e. prognosis) is available. The dataset has been normalised and log2-transformed, and provided as an 'ExpressionSet' object.


CLL <- dRDataLoader(RData = "CLL")


an object of class "ExpressionSet". It has slots for "assayData", "phenoData", and "featureData":

  • assayData: a matrix of 54675 features X 130 samples
  • phenoData: variables describing sample phenotypes (i.e. columns in assayData), including information about samples: "Name" for sample names, "Time" for sampling time to first treatment (years) and "Treatment" for treatment event (1:yes, 0:no)
  • featureData: variables describing features (i.e. rows in assayData), including information about features/genes: "EntrezID" for gene EntrezID, "Symbol" for gene symbol and "Desc" for gene description


Chuang et al. (2012). Subnetwork-based analysis of chronic lymphocytic leukemia identifies pathways that associate with disease progression. Blood, 120(13):2639-49.


CLL <- dRDataLoader(RData='CLL')
'CLL' (from has been loaded into the working environment (at 2018-01-19 12:34:29)
ExpressionSet (storageMode: lockedEnvironment) assayData: 54675 features, 130 samples element names: exprs protocolData: none phenoData sampleNames: GSM977137 GSM977138 ... GSM977266 (130 total) varLabels: Name Time Treatment varMetadata: labelDescription featureData featureNames: 1007_s_at 1053_at ... AFFX-TrpnX-M_at (54675 total) fvarLabels: EntrezID Symbol Desc fvarMetadata: labelDescription experimentData: use 'experimentData(object)' Annotation:
library(Biobase) # extract information about the first 5 samples pData(CLL)[1:5,]
Name Time Treatment GSM977137 CLL1 2.487671 1 GSM977138 CLL2 3.084932 1 GSM977139 CLL3 2.882192 1 GSM977140 CLL4 0.109589 1 GSM977141 CLL5 3.249315 0
# extract information about the first 5 features fData(CLL)[1:5,]
EntrezID Symbol Desc 1007_s_at NA 1053_at 5982 RFC2 replication factor C (activator 1) 2, 40kDa 117_at 3310 HSPA6 heat shock 70kDa protein 6 (HSP70B') 121_at 7849 PAX8 paired box 8 1255_g_at 2978 GUCA1A guanylate cyclase activator 1A (retina)