TCGAbiolinks
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Error in TCGAbiolinks TCGAanalyze_Preprocessing
I am doing the pipeline according this toturial.
clin = GDCquery_clinic("TCGA-BRCA","clinical")
samples = clin[clin$gender=='female',]
miRNA = GDCquery(project='TCGA-BRCA', data.type='miRNA Expression Quantification', data.category="Transcriptome Profiling")
GDCdownload(miRNA, method='api')
dataPrep = GDCprepare(query=miRNA)
data1 = TCGAanalyze_Preprocessing(object = dataPrep,cor.cut = 0.6)
At last step, It comes an error:
Error in (function (classes, fdef, mtable) : unable to find an inherited method for function assays for signature "data.frame"
I found this issue37 report a similar error.
I try to run the command in that issue:
library(SummarizedExperiment)
assays(dataPrep)
the error is still there. May be some errors in my code ?
Hi, @l0o0
I have same issue now in LGG data.
So if you solved this problem, could you give me reply?
I look forward to hearing you.
Thank you.
@diceofeugene This problem was two years ago, I can not remember whether this problem was solved. I am sorry for that.
If the above said problem get solved please share the procedure.
The problem get solved. For this in GDCprepare step set summarizedExperiment = TRUE. This is it, you will not face problem in preprocessing step thereafter.