GDCquery Error in Opening Connection

[KKen357252]

Hi,

My R version is 4.3.0 and my library are up-to-date. When I tried to use the GDCquery to look for data, it shows error in opening connection. The error log is printed as below. It works just fine last week, but when I tried now, it no longer works and I cannot proceed with TCGA dataset. Is there any method on how can I fix this? Thank you in advance

Below are the codes I am trying to run and the error log:

listSamples <- c('TCGA-D6-6516', 'TCGA-T2-A6X2', 'TCGA-BA-4077', 'TCGA-BA-A6DJ', 'TCGA-CV-5442', 'TCGA-CQ-5327', 'TCGA-CX-7086', 'TCGA-CV-6441', 'TCGA-CV-5970', 'TCGA-CV-6952', 'TCGA-T3-A92N', 'TCGA-CR-7390', 'TCGA-CV-7102', 'TCGA-QK-A8Z7', 'TCGA-4P-AA8J', 'TCGA-CR-6491', 'TCGA-BA-6871', 'TCGA-CV-6951', 'TCGA-IQ-A61G', 'TCGA-CN-6020', 'TCGA-CV-6954', 'TCGA-CV-6953', 'TCGA-C9-A47Z', 'TCGA-CV-5439', 'TCGA-QK-AA3K', 'TCGA-CV-5436', 'TCGA-CV-6003', 'TCGA-CV-5977', 'TCGA-CV-6436', 'TCGA-CV-5976', 'TCGA-F7-A61W', 'TCGA-CV-5973', 'TCGA-C9-A480', 'TCGA-CV-6433', 'TCGA-CQ-7065', 'TCGA-CV-5979', 'TCGA-CQ-A4CH', 'TCGA-CV-5971')

TCGA <- GDCquery(project = 'TCGA-HNSC', data.category = 'Gene expression', data.type = 'Gene expression quantification', platform = 'Illumina HiSeq', file.type = 'results', barcode = listSamples, legacy = TRUE )

Error log: o GDCquery: Searching in GDC database

Genome of reference: hg19 Error in open.connection(con, "rb") : cannot open the connection to 'https://api.gdc.cancer.gov/legacy/projects/TCGA-HNSC?expand=summary,summary.data_categories&pretty=true' In addition: Warning message: In open.connection(con, "rb") : cannot open URL 'https://api.gdc.cancer.gov/legacy/projects/TCGA-HNSC?expand=summary,summary.data_categories&pretty=true': HTTP status was '410 Gone'

[JRAnalytics]

Same problem since last Friday! Was working well on last Thursday.

[JRAnalytics]

Try to check the not opening URL and this message came in browser :

"The GDC Legacy Archive is no longer available. For assistance, contact the GDC Help Desk at support@nci-gdc.datacommons.io"

and check that : https://gdc.cancer.gov/news-and-announcements/gdc-legacy-archive-retires

[KKen357252]

Ah I see. If that so, are there any alternative methods to GDC query for analyzing TCGA dataset that you recommend? I am new to the field and this is in fact my first try on analyzing a TCGA dataset and with specific samples. Any recommendation would be much appreciated. Thank you in advance.

[tiagochst]

Legacy database will not exist anymore, we have been updating the package to remove legacy support since last week.

@KKen357252 The code below will acess the data aligned against hg38.

listSamples <- c(
    'TCGA-D6-6516', 'TCGA-T2-A6X2', 'TCGA-BA-4077', 'TCGA-BA-A6DJ', 'TCGA-CV-5442', 'TCGA-CQ-5327',
    'TCGA-CX-7086', 'TCGA-CV-6441', 'TCGA-CV-5970', 'TCGA-CV-6952', 'TCGA-T3-A92N', 'TCGA-CR-7390',
    'TCGA-CV-7102', 'TCGA-QK-A8Z7', 'TCGA-4P-AA8J', 'TCGA-CR-6491', 'TCGA-BA-6871', 'TCGA-CV-6951',
    'TCGA-IQ-A61G', 'TCGA-CN-6020', 'TCGA-CV-6954', 'TCGA-CV-6953', 'TCGA-C9-A47Z', 'TCGA-CV-5439',
    'TCGA-QK-AA3K', 'TCGA-CV-5436', 'TCGA-CV-6003', 'TCGA-CV-5977', 'TCGA-CV-6436', 'TCGA-CV-5976',
    'TCGA-F7-A61W', 'TCGA-CV-5973', 'TCGA-C9-A480', 'TCGA-CV-6433', 'TCGA-CQ-7065', 'TCGA-CV-5979',
    'TCGA-CQ-A4CH', 'TCGA-CV-5971'
)

query <- GDCquery(
    project = 'TCGA-HNSC',
    data.category = "Transcriptome Profiling",
    data.type = "Gene Expression Quantification", 
    workflow.type = "STAR - Counts",
    barcode = listSamples
)
GDCdownload(query = query)
data <- GDCprepare(query = query)

[JRAnalytics]

Well you can tried directy$ly in the data portal UI.

I refer to my issue (here)https://github.com/BioinformaticsFMRP/TCGAbiolinks/issues/578

maybe the code from @tiagochst will help you

[KKen357252]

Thank you very much for the replies. Yes, the code works! Thank you once again and wishing you a good day ahead.