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TCGAbiolinks
http://bioconductor.org/packages/devel/bioc/vignettes/TCGAbiolinks/inst/doc/index.html
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GDCprepare: Error in if (query$data.type == "Masked Intensities" | query$data.category == : missing value where TRUE/FALSE needed #580

Closed OlegsBorodins closed 1 year ago

OlegsBorodins commented 1 year ago

Dear Sir / Madam,

I am currently working with TCGA data and I have run it into an error.

tcga_HNSC_data <- GDCprepare(query_TCGA, summarizedExperiment = TRUE) Error in if (query$data.type == "Masked Intensities" | query$data.category == : missing value where TRUE/FALSE needed

I have tried: TCGAbiolinks ( 2.28.2) TCGAbiolinks ( 2.28.1)

It works for some of the data in TCGA-HNSC (see both examples).

You had a similar issue in https://github.com/BioinformaticsFMRP/TCGAbiolinks/issues/285

I hope you can help me. All the best, OB

Output workflow:

> query_TCGA <- GDCquery(project = 'TCGA-HNSC',
+                        data.category = 'Transcriptome Profiling',
+                        experimental.strategy = 'RNA-Seq',
+                        workflow.type = 'STAR - Counts',
+                        access = 'open',
+                        barcode = c('TCGA-BB-4217-01A-11R-2081-07'
+          
+                        ))
--------------------------------------
o GDCquery: Searching in GDC database
--------------------------------------
Genome of reference: hg38
--------------------------------------------
oo Accessing GDC. This might take a while...
--------------------------------------------
ooo Project: TCGA-HNSC
--------------------
oo Filtering results
--------------------
ooo By access
ooo By experimental.strategy
ooo By workflow.type
ooo By barcode
----------------
oo Checking data
----------------
ooo Checking if there are duplicated cases
ooo Checking if there are results for the query
-------------------
o Preparing output
-------------------
> getResults(query_TCGA)
                                      id data_format                        cases access
474 75b8e891-29bb-4993-b867-cf65aa85c8ed         TSV TCGA-BB-4217-01A-11R-2081-07   open
                                                                      file_name                         submitter_id           data_category
474 33f30e2c-ec0d-469d-a23d-0941645139e5.rna_seq.augmented_star_gene_counts.tsv 6b29e8e8-72a0-4819-b657-3aa3114c9d52 Transcriptome Profiling
               type file_size                 created_datetime                           md5sum                 updated_datetime
474 gene_expression   4247546 2021-12-13T18:42:20.012845-06:00 9975b18b72e6cfa0445c8b6845606d53 2022-01-19T12:38:14.995174-06:00
                                 file_id                      data_type    state experimental_strategy version data_release   project
474 75b8e891-29bb-4993-b867-cf65aa85c8ed Gene Expression Quantification released               RNA-Seq       1  32.0 - 37.0 TCGA-HNSC
                             analysis_id analysis_state                             analysis_submitter_id
474 b9b81bc9-293b-4d3c-b302-d6f5a6617116       released 33f30e2c-ec0d-469d-a23d-0941645139e5_star__counts
                                                                                                                          analysis_workflow_link
474 https://github.com/NCI-GDC/gdc-rnaseq-cwl/blob/5d8c131bbff59fb0c969217fc1d44e6d1503cd1f/rnaseq-star-align/star2pass.rnaseq_harmonization.cwl
    analysis_workflow_type                analysis_workflow_version   sample_type is_ffpe cases.submitter_id sample.submitter_id
474          STAR - Counts 5d8c131bbff59fb0c969217fc1d44e6d1503cd1f Primary Tumor      NA       TCGA-BB-4217    TCGA-BB-4217-01A
> destfile_1<- "C:/Users/0.13/Desktop/TCGA_raw_data/RNA_Expression/"
> GDCdownload(query_TCGA,directory = destfile_1)
Downloading data for project TCGA-HNSC
Of the 1 files for download 1 already exist.
All samples have been already downloaded
> tcga_brca_data <- GDCprepare(query_TCGA, summarizedExperiment = TRUE)
Error in if (query$data.type == "Masked Intensities" | query$data.category ==  : 
  missing value where TRUE/FALSE needed
> gdcprojects <- getGDCprojects()
> getProjectSummary('TCGA-HNSC')
$file_count
[1] 26901

$data_categories
  file_count case_count               data_category
1       3709        528            Sequencing Reads
2       2858        528                 Biospecimen
3       4340        526       Copy Number Variation
4       8263        528 Simple Nucleotide Variation
5       2270        528     Transcriptome Profiling
6       1740        528             DNA Methylation
7       1103        528                    Clinical
8       2264        521        Structural Variation
9        354        354          Proteome Profiling

$case_count
[1] 528

$file_size
[1] 7.174608e+13

> query_TCGA <- GDCquery(project = 'TCGA-HNSC',
+                        data.category = 'Transcriptome Profiling',
+                        experimental.strategy = 'RNA-Seq',
+                        workflow.type = 'STAR - Counts',
+                        access = 'open',
+                        barcode = c('TCGA-BB-4217-01A-11R-2081-07'
+          
+                        ))
--------------------------------------
o GDCquery: Searching in GDC database
--------------------------------------
Genome of reference: hg38
--------------------------------------------
oo Accessing GDC. This might take a while...
--------------------------------------------
ooo Project: TCGA-HNSC
--------------------
oo Filtering results
--------------------
ooo By access
ooo By experimental.strategy
ooo By workflow.type
ooo By barcode
----------------
oo Checking data
----------------
ooo Checking if there are duplicated cases
ooo Checking if there are results for the query
-------------------
o Preparing output
-------------------
> getResults(query_TCGA)
                                      id data_format                        cases access
474 75b8e891-29bb-4993-b867-cf65aa85c8ed         TSV TCGA-BB-4217-01A-11R-2081-07   open
                                                                      file_name                         submitter_id           data_category
474 33f30e2c-ec0d-469d-a23d-0941645139e5.rna_seq.augmented_star_gene_counts.tsv 6b29e8e8-72a0-4819-b657-3aa3114c9d52 Transcriptome Profiling
               type file_size                 created_datetime                           md5sum                 updated_datetime
474 gene_expression   4247546 2021-12-13T18:42:20.012845-06:00 9975b18b72e6cfa0445c8b6845606d53 2022-01-19T12:38:14.995174-06:00
                                 file_id                      data_type    state experimental_strategy version data_release   project
474 75b8e891-29bb-4993-b867-cf65aa85c8ed Gene Expression Quantification released               RNA-Seq       1  32.0 - 37.0 TCGA-HNSC
                             analysis_id analysis_state                             analysis_submitter_id
474 b9b81bc9-293b-4d3c-b302-d6f5a6617116       released 33f30e2c-ec0d-469d-a23d-0941645139e5_star__counts
                                                                                                                          analysis_workflow_link
474 https://github.com/NCI-GDC/gdc-rnaseq-cwl/blob/5d8c131bbff59fb0c969217fc1d44e6d1503cd1f/rnaseq-star-align/star2pass.rnaseq_harmonization.cwl
    analysis_workflow_type                analysis_workflow_version   sample_type is_ffpe cases.submitter_id sample.submitter_id
474          STAR - Counts 5d8c131bbff59fb0c969217fc1d44e6d1503cd1f Primary Tumor      NA       TCGA-BB-4217    TCGA-BB-4217-01A

> GDCdownload(query_TCGA,directory = destfile_1)
Downloading data for project TCGA-HNSC
GDCdownload will download: 4.247546 MB
Downloading as: 33f30e2c-ec0d-469d-a23d-0941645139e5.rna_seq.augmented_star_gene_counts.tsv
  |===========================================================================================================================================| 100%
> tcga_HNSC_data <- GDCprepare(query_TCGA, summarizedExperiment = TRUE)
Error in if (query$data.type == "Masked Intensities" | query$data.category ==  : 
  missing value where TRUE/FALSE needed

xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

HOWEVER WITH SOME DATA SETS IT WORKS, FOR EXAMPLE:

xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

> query_TCGA <- GDCquery(project = 'TCGA-HNSC',
+                        data.category = 'Transcriptome Profiling',
+                        experimental.strategy = 'RNA-Seq',
+                        workflow.type = 'STAR - Counts',
+                        access = 'open',
+                        barcode = c('TCGA-CV-7177-11A-01R-2016-07'
+          
+                        ))
--------------------------------------
o GDCquery: Searching in GDC database
--------------------------------------
Genome of reference: hg38
--------------------------------------------
oo Accessing GDC. This might take a while...
--------------------------------------------
ooo Project: TCGA-HNSC
--------------------
oo Filtering results
--------------------
ooo By access
ooo By experimental.strategy
ooo By workflow.type
ooo By barcode
----------------
oo Checking data
----------------
ooo Checking if there are duplicated cases
ooo Checking if there are results for the query
-------------------
o Preparing output
-------------------
> getResults(query_TCGA)
                                    id data_format                        cases access
1 a40e28c3-b3ed-4edf-bfce-71dfb740e8a6         TSV TCGA-CV-7177-11A-01R-2016-07   open
                                                                    file_name                         submitter_id           data_category
1 d8bb9aab-ed89-4087-b0dc-0a43d06e3256.rna_seq.augmented_star_gene_counts.tsv beb324c4-c014-40fa-9b47-117b47f71079 Transcriptome Profiling
             type file_size                 created_datetime                           md5sum                 updated_datetime
1 gene_expression   4230911 2021-12-13T19:11:03.296681-06:00 33ef0d6b659ccc743526d4593be7a8ca 2022-01-19T12:38:14.995174-06:00
                               file_id                      data_type    state experimental_strategy version data_release   project
1 a40e28c3-b3ed-4edf-bfce-71dfb740e8a6 Gene Expression Quantification released               RNA-Seq       1  32.0 - 37.0 TCGA-HNSC
                           analysis_id analysis_state                             analysis_submitter_id
1 a1beed3e-adac-4a25-9dee-d3a841e9ae1a       released d8bb9aab-ed89-4087-b0dc-0a43d06e3256_star__counts
                                                                                                                        analysis_workflow_link
1 https://github.com/NCI-GDC/gdc-rnaseq-cwl/blob/5d8c131bbff59fb0c969217fc1d44e6d1503cd1f/rnaseq-star-align/star2pass.rnaseq_harmonization.cwl
  analysis_workflow_type                analysis_workflow_version         sample_type is_ffpe cases.submitter_id sample.submitter_id
1          STAR - Counts 5d8c131bbff59fb0c969217fc1d44e6d1503cd1f Solid Tissue Normal      NA       TCGA-CV-7177    TCGA-CV-7177-11A
> GDCdownload(query_TCGA,directory = destfile_1)
Downloading data for project TCGA-HNSC
GDCdownload will download: 4.230911 MB
Downloading as: d8bb9aab-ed89-4087-b0dc-0a43d06e3256.rna_seq.augmented_star_gene_counts.tsv
  |===========================================================================================================================================| 100%
> tcga_HNSC_data <- GDCprepare(query_TCGA, summarizedExperiment = TRUE)
|=========================================================================================================================|100%                      Completed after 0 s 
Starting to add information to samples
 => Add clinical information to samples
 => Adding TCGA molecular information from marker papers
 => Information will have prefix 'paper_' 
hnsc subtype information from:doi:10.1038/nature14129
Available assays in SummarizedExperiment : 
  => unstranded
  => stranded_first
  => stranded_second
  => tpm_unstrand
  => fpkm_unstrand
  => fpkm_uq_unstrand
OlegsBorodins commented 1 year ago

Additionally, I have also checked: devtools::install_github("BioinformaticsFMRP/TCGAbiolinks")

TCGAbiolinks (2.29.0)

And my version of R : 4.3.0

tiagochst commented 1 year ago

You need to specify the same directory you used in GDCdownload in GDCprepare.

GDCdownload(query_TCGA,directory = destfile_1)
tcga_HNSC_data <- GDCprepare(query_TCGA, summarizedExperiment = TRUE,directory = destfile_1)
OlegsBorodins commented 1 year ago

Thx!