Tiago Chedraoui Silva

Hi, Which version of TCGAbiolinks are you using? This data is controlled. This should not be accessible without a token. Also the data seems to be either a maf file...

@DarioS I don't have a windows machine to test it right now. But could you provide the full query, please?

@DarkHe007 The miRNA files in the legacy database had two alternatives. I don't remember the difference between them. But you need to set the `file.type argument`. For `hg19.mirna.quantification` files ```...

I'll check the count and the duplicated sample. I did not touch that function for a long time.

It seems TCGA-OV has 608 cases, but only 587 have clinical data. The numbers are the same from GDC data portal as shown below: Example of case missing clinical data:...

I suggest using the indexed data: `clinical.indexed

Which version of TCGAbiolinks do you have installed? It seems it is an old one. Could you please update it from Github with: ``` withr::with_envvar(c(R_REMOTES_NO_ERRORS_FROM_WARNINGS="true"), remotes::install_github('BioinformaticsFMRP/TCGAbiolinks') ) ```

The indexed data is parsed from the XML files. It seems there is a problem with the parsing. You can get that information in the Biotab or XML. ``` query

Hello, The isoform data available in GCD were initially available only for the miRNA pipeline https://docs.gdc.cancer.gov/Data/Bioinformatics_Pipelines/miRNA_Pipeline/ Did you check the legacy database?

Yes, I am still updating the package. It might be stable in the next few days. I updated the gene information to use GENCODE v36 as GDC is now using....