Can download only Counts files. Cannot download FPKM and FPKM-UQ files

BioinformaticsFMRP / TCGAbiolinksGUI

TCGAbiolinksGUI code development for R/Bioconductor submission http://tcgabiolinks.fmrp.usp.br:3838/

http://bioinformaticsfmrp.github.io/TCGAbiolinksGUI

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Can download only Counts files. Cannot download FPKM and FPKM-UQ files #31

Open kokyriakidis opened 7 years ago

kokyriakidis commented 7 years ago

When I try to download anything else than Count type files I get this type of error. I am talking about HNSC files with clinical data box checked.

Error

Error while preparing the files Error in GDCprepare(query, save = TRUE, save.filename = filename, summarizedExperiment = as.logical(isolate({: I couldn't find all the files from the query. Please check if the directory parameter right or GDCdownload downloaded the samples.

Is it a bug?

tiagochst commented 7 years ago

Hello,

It worked for me.

Please, could you send the sessionInfo()?

Also, which version do you have installed. I believe Bioconductor does not have the last version. I'm trying to update the Bioconductor version, but apparently there is a problem with their windows server.

devtools::install_github('BioinformaticsFMRP/TCGAbiolinks')
devtools::install_github('BioinformaticsFMRP/TCGAbiolinksGUI')
devtools::install_github('tiagochst/ELMER')

kokyriakidis commented 7 years ago

Ok now! The update fixed it!

Do you know how can I download Methylation data and miRNA data and GeneExp data for the same patients?

tiagochst commented 6 years ago

For the same patients you can subset by barcode. But not all of them might have all data.