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A package for researchers in mainland China to downlaod the GEO dataset, which is just a replacement of getGEO function from GEOquery package.
Install the development version from Github:
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("GEOquery")
library(remotes)
url='https://gitee.com/jmzeng/GEOmirror.git'
install_git(url)
If it failed, just because your bad internet connection. You can also download this project directly into your computer, and then install it locally.
use it to download GEO dataset, as below :
library(GEOquery)
library(GEOmirror)
eSet=geoChina('GSE1009')
eSet=geoChina('GSE27533')
eSet=geoChina('GSE95166')
Once you download the ExpressionSet of GEO dataset, you can access the expression matrix and phenotype data:
library(GEOquery)
library(GEOmirror)
## download GSE95166 data
# https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE95166
#eSet=getGEO('GSE95166', destdir=".", AnnotGPL = F, getGPL = F)[[1]]
library(GEOmirror)
eSet=geoChina('GSE95166')
eSet
eSet=eSet[[1]]
probes_expr <- exprs(eSet);dim(probes_expr)
head(probes_expr[,1:4])
boxplot(probes_expr,las=2)
## pheno info
phenoDat <- pData(eSet)
head(phenoDat[,1:4])
# https://www.ncbi.nlm.nih.gov/pubmed/31430288
groupList=factor(c(rep('npc',4),rep('normal',4)))
table(groupList)
eSet@annotation
# GPL15314 Arraystar Human LncRNA microarray V2.0 (Agilent_033010 Probe Name version)
The simple example for downstream analysis of expression profiling by array:
genes_expr=probes_expr
library("FactoMineR")
library("factoextra")
dat.pca <- PCA(t(genes_expr) , graph = FALSE)
dat.pca
fviz_pca_ind(dat.pca,
geom.ind = "point",
col.ind = groupList,
addEllipses = TRUE,
legend.title = "Groups"
)
library(limma)
design=model.matrix(~factor(groupList))
design
fit=lmFit(genes_expr,design)
fit=eBayes(fit)
DEG=topTable(fit,coef=2,n=Inf)
head(DEG)
# We observed that 2107 lncRNAs were upregulated
# while 2090 lncRNAs were downregulated by more than 2-fold,
# NKILA among these downregulated lncRNAs (Fig 1A, GSE95166).
## for volcano plot
df=DEG
attach(df)
df$v= -log10(P.Value)
df$g=ifelse(df$P.Value>0.05,'stable',
ifelse( df$logFC >1,'up',
ifelse( df$logFC < -1,'down','stable') )
)
table(df$g)
df$name=rownames(df)
head(df)
library(ggpubr)
ggpubr::ggscatter(df, x = "logFC", y = "v", color = "g",size = 0.5,
label = "name", repel = T,
label.select =head(rownames(df)),
palette = c("#00AFBB", "#E7B800", "#FC4E07") )
detach(df)
x=DEG$logFC
names(x)=rownames(DEG)
cg=c(names(head(sort(x),100)),
names(tail(sort(x),100)))
cg
library(pheatmap)
n=t(scale(t(genes_expr[cg,])))
n[n>2]=2
n[n< -2]= -2
n[1:4,1:4]
ac=data.frame(groupList=groupList)
rownames(ac)=colnames(n)
pheatmap(n,show_colnames =F,show_rownames = F,
annotation_col=ac)
Actually, I should change the probe ID to gene names, but it's not this package should do, so I just omit it.
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