error with GDCprepare

[kdpreter]

When I run following script, in the end I get the error message below. How can I solve this problem? Kind regards,

Katleen

query <- GDCquery(project = "TARGET-NBL", data.category = "Transcriptome Profiling", data.type = "Gene Expression Quantification", workflow.type = "HTSeq - Counts", legacy=T) GDCdownload(query, method = "api", chunks.per.download = 10) count_data <- GDCprepare(query)

Starting to add information to samples Adding description to TARGET samples => Add clinical information to samples Error in $<-.data.frame(*tmp*, "sample.aux", value = character(0)) : replacement has 0 rows, data has 2

[tiagochst]

Hello,

HTSeq - Counts is not available in legacy database. Due to that, the first step (GDCquery) should give you an error.

This should work.

query <- GDCquery(project = "TARGET-NBL",
                  data.category = "Transcriptome Profiling",
                  data.type = "Gene Expression Quantification",
                  workflow.type = "HTSeq - Counts")
GDCdownload(query, method = "api", chunks.per.download = 10)
count_data <- GDCprepare(query)

[kdpreter]

Thanks a lot for your reply. Unfortunately, with the script below I still get the error message:

Starting to add information to samples Adding description to TARGET samples => Add clinical information to samples Error in $<-.data.frame(*tmp*, "sample.aux", value = character(0)) : replacement has 0 rows, data has 169

Kind regards,

Katleen

On 29 Jun 2017, at 01:00, Tiago Chedraoui Silva notifications@github.com<mailto:notifications@github.com> wrote:

Hello,

HTSeq - Counts is not available in legacy databasehttps://portal.gdc.cancer.gov/legacy-archive/search/f?filters=%7B%22op%22:%22and%22,%22content%22:%5B%7B%22op%22:%22in%22,%22content%22:%7B%22field%22:%22cases.project.program.name%22,%22value%22:%5B%22TARGET%22%5D%7D%7D,%7B%22op%22:%22in%22,%22content%22:%7B%22field%22:%22cases.project.project_id%22,%22value%22:%5B%22TARGET-NBL%22%5D%7D%7D%5D%7D. Due to that, the first step (GDCquery) should give you an error.

This should work.

query <- GDCquery(project = "TARGET-NBL", data.category = "Transcriptome Profiling", data.type = "Gene Expression Quantification", workflow.type = "HTSeq - Counts") GDCdownload(query, method = "api", chunks.per.download = 10) count_data <- GDCprepare(query)

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/BioinformaticsFMRP/TCGAbiolinks/issues/108#issuecomment-311815495, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AcSAG9F9g302UZtk_MJbNFJW_EFYitLOks5sItsGgaJpZM4ODeRa.