I want to download ESCA and miRNA data, and analyze differentially expression genes according to G staging. But I have a problem with TCGAanalyze_Preprocessing. I run the following code with version 2.8.4:
ooo Check if there are duplicated cases
ooo Check if there results for the query
o Preparing output
GDCdownload(query = query)
Downloading data for project TCGA-ESCA
Of the 195 files for download 195 already exist.
All samples have been already downloaded
esca.hg19.mirbase20<- GDCprepare(query,save = TRUE, save.filename = "escaExphg19mirbase20.rda")
|================================================================================================| 100%Saving file:escaExphg19mirbase20.rda
File saved
dataSubt <- TCGAquery_subtype(tumor = "ESCA")
esca subtype information from:doi:10.1038/nature20805
dataClin <- GDCquery_clinic(project = "TCGA-ESCA","clinical")
dataPrep <- TCGAanalyze_Preprocessing(object = esca.hg19.mirbase20, cor.cut = 0.6)
Error in (function (classes, fdef, mtable) :
unable to find an inherited method for function ‘assays’ for signature ‘"data.frame"’
I found the similar errors, I try to run the command in that issue according to your advise:
library(SummarizedExperiment)
assays(dataPrep)
the error is still not solved.
Then I copied the code from the Case Study n.1, surprisingly, this error did not appear. May be some errors in my code ? How can I solve this problem?
please give me a hand.
Think you very much!
Hi TCGAbiolinks!
I want to download ESCA and miRNA data, and analyze differentially expression genes according to G staging. But I have a problem with TCGAanalyze_Preprocessing. I run the following code with version 2.8.4:
library("TCGAbiolinks", lib.loc="~/R/x86_64-redhat-linux-gnu-library/3.4")