GDCPrepare Error

[isha-ashi]

The following error occurs while trying to download and prepare "Gene expression" data for "TCGA-LIHC". I have many possible old versions like "TCGAbiolinks_2.10.5" that works for my PI and others as well as the development version.

Accessing grch37.ensembl.org to get gene information
Downloading genome information (try:0) Using: Human genes (GRCh37.p13)
Error in fix.by(by.y, y) : 'by' must specify a uniquely valid column

[tiagochst]

Hi,

Could you update to the last version with BiocManager::install("BioinformaticsFMRP/TCGAbiolinks"). I don't think any old versions will be working anymore.

[isha-ashi]

I tried the above solution, and it still throws the error.

[tiagochst]

I'll check, I think I know what it might be.

[tiagochst]

Thanks, I just fixed it. If you reinstall with BiocManager::install("BioinformaticsFMRP/TCGAbiolinks") and restart R it should be working.

[isha-ashi]

Thank you it worked!!

[kkolmus]

Hi,

I am facing the sample problem with the GDCprepare function, which does not allow me to prepare a SummarizedExperiment object and produces the above mentioned error:

Error in fix.by(by.y, y) : 'by' must specify a uniquely valid column

I have been trying to reinstall TCGAbiolinks from Github but then I got:

BiocManager::install("BioinformaticsFMRP/TCGAbiolinks")
Bioconductor version 3.8 (BiocManager 1.30.4), R 3.5.2 (2018-12-20)
Installing github package(s) 'BioinformaticsFMRP/TCGAbiolinks'
Downloading GitHub repo BioinformaticsFMRP/TCGAbiolinks@master
tar: Failed to set default locale
tar: Failed to set default locale
Skipping 1 packages not available: cmprsk
   During startup - Warning messages:
   1: Setting LC_CTYPE failed, using "C" 
   2: Setting LC_TIME failed, using "C" 
   3: Setting LC_MESSAGES failed, using "C" 
   4: Setting LC_MONETARY failed, using "C" 
v  checking for file '/private/var/folders/wj/3pr1s02j28s4yw_pfkbt_38c0000gn/T/RtmpWrZB8t/remotes201446623265/BioinformaticsFMRP-TCGAbiolinks-d5d0980/DESCRIPTION' ...
-  preparing 'TCGAbiolinks':
v  checking DESCRIPTION meta-information ...
-  checking for LF line-endings in source and make files and shell scripts
-  checking for empty or unneeded directories
-  looking to see if a 'data/datalist' file should be added
-  building 'TCGAbiolinks_2.13.3.tar.gz'
   
Error: (converted from warning) Setting LC_CTYPE failed, using "C"
Execution halted
Error: Failed to install 'TCGAbiolinks' from GitHub:
  (converted from warning) installation of package '/var/folders/wj/3pr1s02j28s4yw_pfkbt_38c0000gn/T//RtmpWrZB8t/file20143e7a38d8/TCGAbiolinks_2.13.3.tar.gz' had non-zero exit status

Is there any other way to get the update?

Thanks,

Krzysztof

[AnkitaShukla17]

Please help me regarding the code; I am following TCGAworkflow "https://www.bioconductor.org/packages/release/workflows/vignettes/TCGAWorkflow/inst/doc/TCGAWorkflow.html#transcriptomic_analysis" regarding transcriptomic analysis. I am facing problem at TCGAanalyze_Preprocessing step (My stydy is for colorectal cancer)
Code: dataPrep_COAD<- TCGAanalyze_Preprocessing(object = coad.exp,
cor.cut = 0.6,
datatype = "raw_count",
filename = "COAD_IlluminaHiSeq_RNASeqV2.png")
Error: Error in (function (classes, fdef, mtable) :
unable to find an inherited method for function 'assays' for signature '"data.frame"'.
Please help me to resolve this error. Thanks in advance