Error in module A of TCGA assembler

Question

[bhoomisharma04]

Hi. I am a newbie in the field of bioinformatics. I need to analyze the TCGA data. For that i have downloaded TCGA assembler . However, after loading module A and B , when i try to extract the data, it is continuously giving the error message: Error in fromJSON(jsn) : unexpected character 'c'. I am not sure of the reason behind this error. Please suggest how to rectify the problem.

Thanks in advance

[Kevin Blighe]

Please paste the sequence of commands that you are using. Thank you!

[bhoomisharma04]

Sorry for the late reply. Here's the set of commands i am using:

setwd("C:/Users/admin/Downloads/TCGA-Assembler.2.0.5/TCGA-Assembler")
source("Module_A.R")
source("Module_B.R")
Loading required package: bitops
 filename_biosClin <- DownloadBiospecimenClinicalData(cancerType = "BRCA", saveFolderName = "./ManualExampleData/RawData.TCGA-Assembler/BiospecimenClinicalData", outputFileName = "test")

This is the error returning :

Error in fromJSON(jsn) : unexpected character 'c'
Called from: fromJSON(jsn)
Browse[1]

[mariamcurbelo2061]

Hello.I'm a newbie too. I have the exact same problem, did you managed to figure it out? Because no one answered the post... Thanks in advance

[bhoomisharma04]

Hi. I was using rstudio in windows. I couldn't resolve the problem. Then I switched to Ubuntu. TCGA -Assembler is working fine in the command line.

[Kevin Blighe]

Can you paste your code such that we can have a reproducible example of the problem?

[mariamcurbelo2061]

I just copied the first lines provided from the quickexample provided from TCGS-assembler folder

[mariamcurbelo2061]

source("Module_A.R")
source("Module_B.R")
sPath1 <- "./QuickStartExample/Part1_DownloadedData"
sPath2 <- "./QuickStartExample/Part2_BasicDataProcessingResult"
sPath3 <- "./QuickStartExample/Part3_AdvancedDataProcessingResult"
sCancer <- "BRCA"
vPatientID <- c("TCGA-A7-A13F", "TCGA-AO-A12B", "TCGA-AR-A1AP", "TCGA-AR-A1AQ",
                "TCGA-AR-A1AS", "TCGA-AR-A1AV", "TCGA-AR-A1AW", "TCGA-BH-A0BZ",
                "TCGA-BH-A0DD", "TCGA-BH-A0DG")
path_somaticMutation <-
  DownloadSomaticMutationData(cancerType = sCancer,
                              assayPlatform = "somaticMutation_DNAseq",
                              inputPatientIDs = vPatientID,
                              saveFolderName = sPath1)
list_somaticMutation <-
  ProcessSomaticMutationData(inputFilePath = path_somaticMutation[1],
                             outputFileName = paste(sCancer,
                                                    "somaticMutation",
                                                    sep = "__"),
                             outputFileFolder = sPath2)

[Kevin Blighe]

You mean THIS example?

Also, did you not try to contact either or both of the developers mentioned here: http://www.compgenome.org/TCGA-Assembler/

[mariamcurbelo2061]

And this is what I get on the console

> source("Module_A.R")
> source("Module_B.R")
> sPath1 <- "./QuickStartExample/Part1_DownloadedData"
> sPath2 <- "./QuickStartExample/Part2_BasicDataProcessingResult"
> sPath3 <- "./QuickStartExample/Part3_AdvancedDataProcessingResult"
> sCancer <- "BRCA"
> vPatientID <- c("TCGA-A7-A13F", "TCGA-AO-A12B", "TCGA-AR-A1AP", "TCGA-AR-A1AQ",
+                 "TCGA-AR-A1AS", "TCGA-AR-A1AV", "TCGA-AR-A1AW", "TCGA-BH-A0BZ",
+                 "TCGA-BH-A0DD", "TCGA-BH-A0DG")
> path_somaticMutation <-
+   DownloadSomaticMutationData(cancerType = sCancer,
+                               assayPlatform = "somaticMutation_DNAseq",
+                               inputPatientIDs = vPatientID,
+                               saveFolderName = sPath1)
Error in fromJSON(jsn) : unexpected character 'c'