Question: Error in module A of TCGA assembler
0
gravatar for bhoomisharma04
14 months ago by
United States
bhoomisharma0410 wrote:

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

ADD COMMENTlink modified 14 months ago • written 14 months ago by bhoomisharma0410

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

ADD REPLYlink written 14 months ago by Kevin Blighe41k

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]
ADD REPLYlink modified 14 months ago by Kevin Blighe41k • written 14 months ago by bhoomisharma0410

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

ADD REPLYlink written 3 months ago by mariamcurbelo20610
1

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.

ADD REPLYlink written 3 months ago by bhoomisharma0410

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

ADD REPLYlink written 3 months ago by Kevin Blighe41k

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

ADD REPLYlink modified 3 months ago • written 3 months ago by mariamcurbelo20610
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)
ADD REPLYlink modified 3 months ago • written 3 months ago by mariamcurbelo20610

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/

ADD REPLYlink modified 3 months ago • written 3 months ago by Kevin Blighe41k

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'
ADD REPLYlink modified 3 months ago • written 3 months ago by mariamcurbelo20610
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1503 users visited in the last hour