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TCGAbiolinks
http://bioconductor.org/packages/devel/bioc/vignettes/TCGAbiolinks/inst/doc/index.html
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TCGAbiolinks TCGAanalyze_Preprocessing #284

Open DaydayupNo1 opened 5 years ago

DaydayupNo1 commented 5 years ago

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")

library(SummarizedExperiment) query <- GDCquery(project = "TCGA-ESCA",

  • legacy = TRUE,
  • data.category = "Gene expression",
  • data.type = "miRNA gene quantification",
  • file.type = "hg19.mirbase20"

  • )

    o GDCquery: Searching in GDC database

    Genome of reference: hg19

    oo Accessing GDC. This might take a while...

    ooo Project: TCGA-ESCA

    oo Filtering results

    ooo By data.type ooo By file.type

    oo Checking data

    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!

AnkitaShukla17 commented 5 years ago

Can you please tell how you resolved the above problem, as I am facing same error.

AnkitaShukla17 commented 5 years ago

In GDCprepare set summarizedExperiment = TRUE, the following error will not occur anymore.