Question: (Closed) Error in TCGAbiolinks
gravatar for nazaninhoseinkhan
9 months ago by
Iran, Islamic Republic Of
nazaninhoseinkhan390 wrote:

Dear all, I am trying to do methylation analysis on TCGA data using TCGAbiolinks.

Since I only wanted to use a limited subset of samples, I used their TCGA codes in:

query.met.normal = GDCquery(project = "TCGA-THCA",legacy = TRUE,data.category= "DNA methylation",

platform = "Illumina Human Methylation 450",

barcode = c("TCGA-EM-A3ST-11A-11D-A231-05" ,"TCGA-FY-A3TY-11A-12D-A231-05" , ...)).

After downloading data which were saved in "C:\Users\Administrator\Documents\GDCdata\TCGA-THCA\legacy\DNA_Methylation\Methylation_Beta_Value", I used :

met.normal.450 = GDCprepare(query = query.met.normal,save= TRUE,save.filename = "normalDNAmet450k.rda" ,summarizedExperiment = TRUE),

however I got this error:

Error in rbind(deparse.level,...) numbers of columns of arguments do not match.

Can you guide me to solve this problem?

Kind regards


ADD COMMENTlink modified 7 months ago by Biostar ♦♦ 20 • written 9 months ago by nazaninhoseinkhan390

It is better to post TCGAbiolinks issues on the GitHub page:

ADD REPLYlink written 7 months ago by Kevin Blighe56k

Thanks Kevin, Yes, Tiago Silva helped to to solve this problem

ADD REPLYlink written 7 months ago by nazaninhoseinkhan390

I also get this problem

ADD REPLYlink written 9 months ago by tthloc.stu130
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