Question: Getting RNA expression from TCGA only for these patients IDs
0
gravatar for A
6 months ago by
A3.8k
A3.8k wrote:

Hi

I have been asked to download RNA expression from TCGA only for some tumour IDs like below

Patient_ids Tumor_type
TCGA-IG-A4QS    Esophagus
TCGA-JY-A6FB    Esophagus
TCGA-JY-A938    Esophagus
TCGA-JY-A939    Esophagus

I then tried this R package that returns error

> query <- GDCquery(project = "TCGA-ESCA",
+                   data.category = "Transcriptome Profiling",
+                   data.type = "Gene Expression Quantification", 
+                   workflow.type = "HTSeq - Counts")
Error in value[[3L]](cond) : 
  GDC server down, try to use this package later

Can somebody please help i getting RNA-seq for these samples from TCGA? Thanks in advance

rna-seq tcga R • 252 views
ADD COMMENTlink modified 6 months ago • written 6 months ago by A3.8k
1
gravatar for A
6 months ago by
A3.8k
A3.8k wrote:
query <- GDCquery(project = "TCGA-ESCA",
data.category = "Transcriptome Profiling",
data.type = "Gene Expression Quantification",
workflow.type = "HTSeq - Counts",barcode = c("SAMPLE IDs"),sample.type = "Primary solid Tumor")
GDCdownload(query)
data <- GDCprepare(query)
ADD COMMENTlink written 6 months ago by A3.8k
1

So in summary, you tried again a few hours later and the server was up again, and it now worked.

ADD REPLYlink modified 6 months ago • written 6 months ago by ATpoint34k
1

This isn't an answer. A block of unexplained code doesn't help people in future.

ADD REPLYlink written 6 months ago by Joe16k
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