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Getting RNA expression from TCGA only for these patients IDs

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

tcga r rna-seq
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updated by 1830416019 • 1830416019 • written by zizigolu zizigolu

Have you solved it?Can you give me a hand?wuuwu

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written by 1830416019 • 1830416019

What is your question?

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written by zizigolu zizigolu

1 answer 

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)
• 0 views • link
written by zizigolu zizigolu

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

• 0 views • link
written by ATpoint ATpoint

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

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written by Joe Joe

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