Question: GDCprepare - error
gravatar for vm
5 weeks ago by
vm0 wrote:

Hi! I'm having a problem with the function GDCprepare. GDCquery and GDCdownload work just fine, but I keep getting the following error message when I try to run GDCprepare. Thanks in advance for the help.

library(dplyr) library(DT) library(TCGAbiolinks) library(SummarizedExperiment) query = GDCquery(project = "TCGA-BRCA",data.category = "Transcriptome Profiling",data.type = "Gene Expression Quantification",workflow.type = "HTSeq - Counts",legacy = F,sample.type = c("Primary solid Tumor","Solid Tissue Normal")) mama = GDCprepare(query = query)

|=================================================================================================================================================| 100% 1 MB |=================================================================================================================================================| 100% 1 MB |=================================================================================================================================================| 100% 1 MB |======================================================================================================================================================| 100% Starting to add information to samples => Add clinical information to samples Error in rbindlist(l, use.names, fill, idcol) : Item 2 has 57 columns, inconsistent with item 1 which has 58 columns. If instead you need to fill missing columns, use set argument 'fill' to TRUE.

sessionInfo() R version 3.5.1 (2018-07-02) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows >= 8 x64 (build 9200)

Matrix products: default

locale: [1] LCCOLLATE=PortugueseBrazil.1252 LCCTYPE=PortugueseBrazil.1252 LCMONETARY=PortugueseBrazil.1252 LCNUMERIC=C
[5] LC

attached base packages: [1] parallel stats4 stats graphics grDevices utils datasets methods base

other attached packages: [1] SummarizedExperiment1.10.1 DelayedArray0.6.6 BiocParallel1.14.2 matrixStats0.54.0 Biobase2.40.0
[6] GenomicRanges
1.32.6 GenomeInfoDb1.16.0 IRanges2.14.11 S4Vectors0.18.3 BiocGenerics0.26.0
[11] TCGAbiolinks2.8.4 DT0.4 dplyr_0.7.6

tcgabiolinks gdcprepare • 90 views
ADD COMMENTlink written 5 weeks ago by vm0

The package is outdated. We fixed that problem a month ago. Could you update the package, please with the following command: BiocManager::install("BioinformaticsFMRP/TCGAbiolinks")?

ADD REPLYlink written 4 weeks ago by tiagochst150

Updating the package fixed the problem. Thank you very much, Tiago!

ADD REPLYlink written 10 days ago by vm0

Please use the reprex package to run your code in a reproducible way and formatted. See ?reprex::reprex.

ADD REPLYlink written 4 weeks ago by Marcel Ramos ♦♦ 410

I apologize for the unformatted code. I will use reprex next time, Marcel. Thank you!

ADD REPLYlink written 10 days ago by vm0

See also:

ADD REPLYlink written 4 weeks ago by Marcel Ramos ♦♦ 410
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 216 users visited in the last hour