2025-03-11
Download dataset from GEO.
Setting anotation.
Select samples corresponding to cerebrum and cerebellum.
(ts21=c(grep("T.*21.*cerebrum", as.character(pData(gse1397raw)[,"title"])),
grep("TS21.*cerebellum", as.character(pData(gse1397raw)[,"title"]))))
(eu=c(grep("Euploid.*cerebrum)", as.character(pData(gse1397raw)[,"title"])),
grep("Euploid.*[Cc]erebellum", as.character(pData(gse1397raw)[,"title"]))))
gse1397raw = gse1397raw[,c(eu,ts21)]
colnames0 = colnames(gse1397raw)
Normalize the samples (quantile normalization).
Note that the correspondence between PROBEID and ENTREZID is not 1-1. We have to select one correspondence.
Saving normalized data
This is the data set is tamidata::gse1397.
Usually, we will start our analysis with a data set organized using a Biobase::ExpressionSet. For instance, tamidata::gse1397. It is easy to construct an ExpressionData.