- Pathway and Network Analysis 93
element names: exprs
protocolData: none
phenoData
sampleNames: 01005 01010 ... LAL4 (128 total)
varLabels: cod diagnosis ... date last seen (21 total)
varMetadata: labelDescription
featureData: none
experimentData: use ‘experimentData(object)’
pubMedIds:14684422 16243790
Annotation: hgu95av2
Now, you know that ALL is an object of ExpressionSet and annotated under
the microarray platform hgu95av. To fetch the expression matrix in ALL of
the class ExpressionSet, use the function exprs():
DATA.ALL<- exprs(ALL)
Next, you can assign a matrix named DATA.ALL from the object ALL,
where each row corresponds to a probe name and each column represents a
patient (sample).
- Probe-to-gene conversion of the gene expression
dataset
To facilitate the subsequent analyses, you can transform the probe sets of
any microarray platform into the corresponding gene symbols if a mapping
is available. To this end, considering the fact that ALL is annotated under
the microarray platform hgu95av, you can load the R package hgu95av.db
which has been downloaded beforehand:
library(hgu95av.db)
You can check all available objects in hgu95av.db using the command:
ls(“package:hgu95av2.db”)
You can use two Bimap objects hgu95av2ENTREZID and hgu95av2SYM
BOL in this package, which store the mappings between probe labels
and Entrez gene identifiers^3 and between probe labels and gene symbols,
respectively, to get the mapped Entrez IDs and gene symbols (NA is assigned
if there’s no mapping for that probe):
ez<- mget(row.names(DATA.ALL), envir=hgu95av2ENTREZID)
ez<- as.character(sapply(ez, “[”))
sb<- mget(row.names(DATA.ALL), envir=hgu95av2SYMBOL)