Open LeaLe88 opened 7 months ago
Good afternoon,
I am having issues with GDCPrepare with the CPTAC-3 dataset for scRNA-seq data.
I have successfully downloaded the data with
#Query the data query.exp <- GDCquery( project = "CPTAC-3", data.category = "Transcriptome Profiling", experimental.strategy = "scRNA-Seq", workflow.type="CellRanger - 10x Filtered Counts", data.type = "Gene Expression Quantification", sample.type = c("Primary Tumor") ) #Get results output.query<-getResults(query.exp) #Downloads the data #GDCDownload(query.exp) GDCdownload( query = query.exp, files.per.chunk = 100 )
However, it is giving me the following error when trying to use GDCPrepare with GDCprepare(query.exp) :
t::Read10X(data.dir = gsub("\\.tar\\.gz", "", f)) : Directory provided does not exist Error in if (value == n) { : argument is of length zero
Do you have any idea what could be the issue? Maybe for scRNA seq I cant use the summarized Experiment?
Thanks a lot, Lea
Good morning,
Has anyone an idea on this?
Good afternoon,
I am having issues with GDCPrepare with the CPTAC-3 dataset for scRNA-seq data.
I have successfully downloaded the data with
However, it is giving me the following error when trying to use GDCPrepare with GDCprepare(query.exp) :
Do you have any idea what could be the issue? Maybe for scRNA seq I cant use the summarized Experiment?
Thanks a lot, Lea