Created
March 28, 2018 23:22
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| gset <- getGEO('GSE26253')[[1]] | |
| pData(gset) | |
| gset2 <- getGEO('GSE15460')[[1]] | |
| pData(gset2) | |
| write.csv(pData(gset), file = "GSE26253PHENO.csv") | |
| write.csv(pData(gset2), file = "GSE15460PHENO.csv") | |
| ## | |
| data.matrix(gset@featureData@data$Entrez_Gene_ID) | |
| data.matrix(gset@featureData@data$Probe_Id) | |
| data.matrix(gset2@featureData@data$ENTREZ_GENE_ID) | |
| data.matrix(gset2@featureData@data$ID) | |
| fgset <- fData(gset) | |
| tgset <- exprs(gset) | |
| cnames <- c( c("ID", "EntrezID"), colnames(tgset)) | |
| write.csv(data.frame(fgset$ID, fgset$Entrez_Gene_ID, tgset), file = "GSETExpression.csv", row.names = FALSE, col.names = cnames, sep = "/t") | |
| fgset2 <- fData(gset2) | |
| tgset2 <- exprs(gset2) | |
| cnames2 <- c( c("ID", "EntrezID"), colnames(tgset2)) | |
| write.csv(data.frame(fgset2$ID, fgset2$Entrez_Gene_ID, tgset2), file = "GSETExpression2.csv", row.names = FALSE, col.names = cnames2, sep = "/t") | |
| source("http://bioconductor.org/biocLite.R") | |
| biocLite("genefilter") | |
| library(genefilter) | |
| source("https://bioconductor.org/biocLite.R") | |
| biocLite("illuminaHumanWGDASLv3.db") | |
| library("illuminaHumanWGDASLv3.db") | |
| library(MASS) | |
| gN <- sample(ls(illuminaHumanWGDASLv3ENTREZID, 17418)) | |
| testStat <- lapply(illuminaHumanWGDASLv3ENTREZID, coefficient.variation(illuminaHumanWGDASLv3ENTREZID)) | |
| findLargest(gN, testStat, data = "illuminaHumanWGDASLv3") |
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