Hi there,

I always used TCGAbiolinks to get raw count for TCGA projects like below:

    expquery <- GDCquery(project = "TCGA-KIRC",
                     data.category = "Transcriptome Profiling",
                     data.type = "Gene Expression Quantification",
                     workflow.type = "HTSeq - Counts")
    GDCdownload(expquery,directory = "GDCdata")
    expquery2 <- GDCprepare(expquery,directory = "GDCdata",summarizedExperiment = T)
    expMatrix <- TCGAanalyze_Preprocessing(expquery2)

However, it does not work today and it seems there is no HTSeq - Counts 

    Error in GDCquery(project = "TCGA-KIRC", data.category = "Transcriptome Profiling",  : 
      Please set a valid workflow.type argument from the list below:
      => STAR - Counts

Therefore, I used STAR - Counts to download the data, which has completely different format of what I downloaded before using HTSeq - Count. The expression matrix for each sample has more columns including fpkm_unstranded and tpm_unstranded. 

Actually the data downloaded using STAR - Counts is much more useful but I do not know how to extract the files to a readable expression matrix (ENSEMBL ID as rownames and TCGA tumor barcode as column names) because the GDCprepare() function fails to work on it:

    expquery2 <- GDCprepare(expquery,directory = "GDCdata",summarizedExperiment = T)
    |                                                          |  0%                      
    Error in readr::read_tsv(file = f, col_names = TRUE, progress = FALSE,  : 
      unused argument (show_col_types = FALSE)
    Error in if (value == n) { : argument is of length zero

Anyone has any solutions? Many thanks in advance!
I have found the solution! 
Just update the TCGAbiolink package from the Github project, here is the link: 
https://github.com/BioinformaticsFMRP/TCGAbiolinks/issues/495

I had some problems during the installation, I had to reinstall some packages to make it work, here they are: 

library(GenomicDataCommons)
library(GenomeInfoDbData)
library(SummarizedExperiment)
library(ExperimentHub)
library(AnnotationHub)

