Question: Error in module A of TCGA assembler
0
gravatar for bhoomisharma04
23 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 23 months ago • written 23 months ago by bhoomisharma0410

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

ADD REPLYlink written 23 months ago by Kevin Blighe53k

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 23 months ago by Kevin Blighe53k • written 23 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 13 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 12 months ago by bhoomisharma0410

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

ADD REPLYlink written 13 months ago by Kevin Blighe53k

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

ADD REPLYlink modified 13 months ago • written 13 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 13 months ago • written 13 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 13 months ago • written 13 months ago by Kevin Blighe53k

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 13 months ago • written 13 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: 1236 users visited in the last hour