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Question: Extract gene expression values from GDCprepare object
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gravatar for enigmargs
16 months ago by
enigmargs0
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 14 months ago by tiagochst110 • written 16 months ago by enigmargs0
0
gravatar for tiagochst
14 months ago by
tiagochst110
Brazil - University of São Paulo/ Los Angeles - Cedars-Sinai Medical Center
tiagochst110 wrote:

Hi,

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: https://www.bioconductor.org/packages/devel/bioc/vignettes/TCGAbiolinks/inst/doc/download_prepare.html

Best regards,

Tiago

ADD COMMENTlink written 14 months ago by tiagochst110
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