geod71810

Cristian Pérez and Guillermo Ayala

2022-06-01

Packages

The data can be found at

library(Biobase)
library(GEOquery)
library(affy)
library(hgu133plus2.db)

Downloading and preprocessing the data

GEOquery::getGEOSuppFiles("GSE71810")
system("tar xvf GSE71810/GSE71810_RAW.tar")
# Reading CEL files to a  affybatch
affybatch = ReadAffy()
system("rm -fr GSE71810")
system("rm *CEL.gz")

Normalization

eset = rma(affybatch)
ExprMatrix = exprs(eset)

Making the ExpressionSet

infoData = new('MIAME',
        name='Johann PD et al.',
        lab='Not Specified',
        contact ='Marcel Kool <m.kool@dkfz.de>',
        title = 'Atypical Teratoid/Rhabdoid Tumors Are Comprised of Three      
        Epigenetic Subgroups with Distinct Enhancer Landscapes.',
        abstract = 'Summary:    B lymphocytes are important mediators of 
adaptive immunity. They drive naïve T cells to different T-helper profiles. 
Th2 responses are implicated in allergic reactions.
The goal of this study was to characterize the gene expression profile of B 
cells under Th2-skewing conditions.
    
Overall design  B lymphocytes were isolated from human tonsils and cultured 
for 24 hours under Th2-skewing stimulation (anti-CD40 and IL4 treatment) or 
with no stimulation.
RNA was isolated from 4 biological replicates for each condition. 8 samples 
in total were hybridized to Affymetrix gene expression microarrays.
variable: treatment: antiCD40-IL4: antiCD40-IL4_1, antiCD40-IL4_2, antiCD40-IL4_3, antiCD40-IL4_4
variable: treatment: unstimulated: Control_1, Control_2, Control3, Control_4
repeat: biological replicate: antiCD40-IL4_1, antiCD40-IL4_2, antiCD40-IL4_3, antiCD40-IL4_4 repeat: biological replicate: Control_1, Control_2, Control3,
Control_4',
        url = 'http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-71810/')


pd0 = data.frame(type =  factor(c(0,1,0,1,0,1,0,1),
                                levels = 0:1,labels=c("control","treatment")))
rownames(pd0) = colnames(ExprMatrix)
metadatos = data.frame(labelDescription = colnames(pd0),row.names=colnames(pd0))
datosfenotipo = new("AnnotatedDataFrame", data = pd0,
    varMetadata = metadatos)
geod71810  = new("ExpressionSet",
                exprs=ExprMatrix,
                phenoData = datosfenotipo,
                experimentData = infoData,
                annotation='hgu133plus2')

Adding identifiers

a = AnnotationDbi::select(hgu133plus2.db::hgu133plus2.db,
                          keys=featureNames(geod71810),                          column=c("ENTREZID","ENSEMBL","GENENAME"),keytype="PROBEID")
b = match(featureNames(geod71810),a[,"PROBEID"])
fData(geod71810) = a[b,]
dim(geod71810)
dim(fData(geod71810))
save(geod71810,file="geod71810.rda")