Question: GDCprepare - error
0
gravatar for vm
5 weeks ago by
vm0
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
TIME=Portuguese_Brazil.1252

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
2

The package is outdated.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
1

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
1

See also: https://support.bioconductor.org/p/122736/

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