问题遇到的现象和发生背景
想问一下我这样下载的数据是只经过FPKM标准化的还是经过标准化然后求log之后的，谢谢
问题相关代码，请勿粘贴截图
library(BiocManager)
library(TCGAbiolinks)
library(SummarizedExperiment)
query_1 <- GDCquery(project = "TCGA-LUAD",
legacy = TRUE,
platform = "Illumina HiSeq",
file.type = "normalized_results",
experimental.strategy = "RNA-Seq",
data.category = "Gene expression",
data.type = "Gene expression quantification")
GDCdownload(query_1)
dataPrep1<-GDCprepare(query=query_1)
expdat<-assay(dataPrep1)
dim(expdat)
head(expdat)
samplesDown <- getResults(query,cols=c("cases"))
dataSmTP <- TCGAquery_SampleTypes(barcode = samplesDown,
typesample = "TP")
dataSmNT <- TCGAquery_SampleTypes(barcode = samplesDown,
typesample = "NT")
barcode = c(dataSmTP, dataSmNT)
dataAssy = GDCprepare(query, summarizedExperiment = F)
