Tiago Chedraoui Silva
Tiago Chedraoui Silva
The information about the TCGA barcode can be found at https://docs.gdc.cancer.gov/Encyclopedia/pages/TCGA_Barcode/ This should help you match the data and metadata. TCGA-3C-AAAU is the patient, TCGA-3C-AAAU-01 is the primary tumor sample...
Yes, I should be dead in the indexed data. There are some inconsistencies in the indexed data. I will report it to the GDC team.
Here is the GDC answer: > Hi Tiago Chedraoui Silva, > Sorry for the delay but we had to finish our investigate. You are correct, their is an issue. The...
Hello, sorry for the delay. They told me it was fixed, but I found 9 cases that are still wrong. I just reported them.
I checked last week that specific inconsistency and it was solved. I’ll try to make a script to check all cases just to be sure. But I would guess that...
The problem is the same sample has two platforms (Illumina GA and Illumina. HiSeq). The package does not to handle duplicated samples in the prepare step, because that would require...
Projects not successful prepared: - TCGA-PAAD - TCGA-SKCM
Breaking probably due files with no daa
@biosyssun You need to specify the platform. Also, could you updated it. ``` query.meth
Do you have the latest version installed? BiocManager::install("BioinformaticsFMRP/TCGAbiolinksGUI.data")BiocManager::install("BioinformaticsFMRP/TCGAbiolinks") On Sat, Apr 30, 2022, 10:33 PM bioinfofuns ***@***.***> wrote: > [image: 图片] > > Walk through the case study of TCGAbiolinks,...