Hi everybody,

I have got new error by using TCGAbiolinks today. I tried same commands in tutorial but got the error below. Why does it give this error? Is it possible that TCGA database has been changed again? How can we fix this problem? Is there a problem at package commands working at background?

> query <- GDCquery(project = "TCGA-GBM",
                  data.category = "Gene expression",
                  data.type = "Gene expression quantification",
                  platform = "Illumina HiSeq", 
                  file.type  = "normalized_results",
                  experimental.strategy = "RNA-Seq",
                  barcode = c("TCGA-14-0736-02A-01R-2005-01", "TCGA-06-0211-02A-02R-2005-01"),
                  legacy = TRUE)
> GDCdownload(query, method = "api", chunks.per.download = 10)
> data <- GDCprepare(query)

--------------------------------------
o GDCquery: Searching in GDC database
--------------------------------------
Genome of reference: hg19
Warning: 40 parsing failures.
row # A tibble: 5 x 5 col     row   col  expected     actual                                                        file expected   <int> <chr>     <chr>      <chr>                                                       <chr> actual 1     1  <NA> 8 columns 71 columns 'https://gdc-api.nci.nih.gov/projects?size=1000&format=tsv' file 2     2  <NA> 8 columns 71 columns 'https://gdc-api.nci.nih.gov/projects?size=1000&format=tsv' row 3     3  <NA> 8 columns 71 columns 'https://gdc-api.nci.nih.gov/projects?size=1000&format=tsv' col 4     4  <NA> 8 columns 71 columns 'https://gdc-api.nci.nih.gov/projects?size=1000&format=tsv' expected 5     5  <NA> 8 columns 71 columns 'https://gdc-api.nci.nih.gov/projects?size=1000&format=tsv'
... ................. ... .............................................................................................. ........ .............................................................................................. ...... .................. [... truncated]

|disease_type.2              |disease_type.5                      |disease_type.4       |disease_type.6               |
|:---------------------------|:-----------------------------------|:--------------------|:----------------------------|
|NA                          |NA                                  |NA                   |NA                           |
|NA                          |NA                                  |NA                   |NA                           |
...
|Thymic Epithelial Neoplasms |Complex Mixed and Stromal Neoplasms |Basal Cell Neoplasms |Ductal and Lobular Neoplasms |
|NA                          |NA                                  |NA                   |NA                           |
|NA                          |NA                                  |NA                   |NA                           |
...
Error in checkProjectInput(project) :
  Please set a valid project argument from the column id above. Project TCGA-GBM was not found.
In addition: Warning messages:
1: Unnamed `col_types` should have the same length as `col_names`. Using smaller of the two.
2: In rbind(names(probs), probs_f) :
  number of columns of result is not a multiple of vector length (arg 1)
3: Unknown or uninitialised column: 'project_id'.
4: Unknown or uninitialised column: 'project_id'.

Thanks in advance.

Talip.

I got the same error using a query that worked a few weeks ago using "TCGA-BRCA". There is a version of TCGABiolinks on github that appears to have solved the issue. You can find it here:

https://github.com/BioinformaticsFMRP/TCGAbiolinks

On my platform, installation required:

install.packages("devtools", dependencies = TRUE)

install.packages("robustbase")

devtools::install_github(repo = "BioinformaticsFMRP/TCGAbiolinks")