Question: Extract gene expression values from GDCprepare object
gravatar for enigmargs
12 months ago by
enigmargs0 wrote:

Hello, I am trying to download gene expressions values from TCGA-GBM project from GDC using TCGAbiolinks using the example code below;

query <- GDCquery(project = "TCGA-GBM", legacy = TRUE,
        data.category = "Gene expression", data.type = "Gene expression quantification",
        platform = "Illumina HiSeq", file.type = "normalized_results", experimental.strategy = "RNA-Seq")

GDCdownload(query); GDCprepare(query, save=T)

But, I am unable to save the object from GDCprepare. Should the object from GDCprepare result in a dataframe? (It's not a dataframe when I checked it). If so how to access the gene expression values within them? Is it possible to extract only gene expression and patient ID from S4 object resulting from GDCprepare

Any help is much appreciated.


ADD COMMENTlink modified 11 months ago by tiagochst110 • written 12 months ago by enigmargs0
gravatar for tiagochst
11 months ago by
Brazil - University of São Paulo/ Los Angeles - Cedars-Sinai Medical Center
tiagochst110 wrote:


The default GDCprepare output is a SummarizedExperiment (SE) object, but you can also set to output the data frame.

The main difference is the the SE  has gene information (start, end and others) and sample information.

There are some examples here:

Best regards,


ADD COMMENTlink written 11 months ago by tiagochst110
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