Question: TCGAbiolinks query error
0
gravatar for gaiusjaugustus
2.7 years ago by
University of Arizona
gaiusjaugustus0 wrote:

I am trying to get a list of samples that have certain datasets.  My goal is to use TCGAbiolinks to query the database and then will compare queries from different data types (e.g. Mutation, RNAseq, and Methylation450).  This will allow me to identify cases that have multiple data types and only download the data from those cases.

 

I ran the following command:

# All DNA methylation data for TCGA-COAD and TCGA-READ
query.meth <- GDCquery(project = c("TCGA-COAD","TCGA-READ"),
                      legacy = TRUE,
                      data.category = "DNA methylation",
                      platform = c("HumanMethylation450", "HumanMethylation27"))

And am getting the following error + traceback.

the condition has length > 1 and only the first element will be usedthe condition has length > 1 and only the first element will be used
 Hide Traceback
Error: lexical error: invalid char in json text. https://gdc-api.nci.nih.gov/leg (right here) ------^
7.parse_string(txt, bigint_as_char)
6.parseJSON(txt, bigint_as_char)
5.fromJSON_string(txt = txt, simplifyVector = simplifyVector, simplifyDataFrame = simplifyDataFrame, simplifyMatrix = simplifyMatrix, flatten = flatten, ...)
4.fromJSON(url, simplifyDataFrame = TRUE)
3.getProjectSummary(project, legacy)
2.checkDataCategoriesInput(project, data.category, legacy)
1.GDCquery(project = c("TCGA-COAD", "TCGA-READ"), legacy = TRUE, data.category = "DNA methylation", platform = c("HumanMethylation450", "HumanMethylation27"))

 

Any help on this would be appreciated.

tcgabiolinks • 647 views
ADD COMMENTlink written 2.7 years ago by gaiusjaugustus0
1

The software currently has some errors. Hopefully, the developers will fix it soon and your problem will be resolved.

ADD REPLYlink written 2.7 years ago by Dario Strbenac1.5k
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