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modarzi
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@modarzi-16296
Last seen 4.2 years ago
Hi,
I wanted to run below query via GDCquey:
query <- GDCquery(project = "TCGA-BRCA",sample.type = "Primary solid Tumor", data.category = "Transcriptome Profiling", data.type = "Gene Expression Quantification",workflow.type = "HTSeq - FPKM-UQ") #but I got below error: Error in value[3L] : GDC server down, try to use this package later
my sessioninfo() is :
R version 3.5.0 (2018-04-23) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows >= 8 x64 (build 9200) Matrix products: default locale: [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 [3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C [5] LC_TIME=English_United States.1252
I appreciate if you share your comment with me.
Best Regards,
Mohammad
Try Now, the server is running!
Hi,
Thanks for your comment. I tried now but unfortunately I received below message again:
I don't know what is my problem? my query has problem or package needs some update or GDC server really is done?
I appreciate if you share your comment with me.
Best Regards,
Mohammad
GDC server is not down. On my pc your command run!
but unfortunately for me give below error again:
Try to run this command:
What's your response?
I run this command and got these results:
Try to reinstall TCGAbiolink with this command:
Thanks for your comment. I reinstalled it again and downloading was started based on below message:
But after downloading 130 MB data I received below message for more than 20 times:
Downloading: 130 MB <simpleWarning in file.create(to[okay]): cannot create file 'GDCdata/TCGA-SARC/harmonized/Transcriptome_Profiling/Gene_Expression_Quantification/c4b3ad46-a679-4ab8-9734-fed35846e691/e9d959e9-5e2d-4652-9ba4-4aeb1e7459be.FPKM-UQ.txt.gz', reason 'No such file or directory'>
<simpleWarning in file.create(to[okay]): cannot create file 'GDCdata/TCGA-SARC/harmonized/Transcriptome_Profiling/Gene_Expression_Quantification/9ec43d2a-bd49-434d-86a1-bd0cf7171dc2/d184d4f3-dc4e-4643-86b8-20dfaf6ee653.FPKM-UQ.txt.gz', reason 'No such file or directory'>
.
.
.
so when I wanted to run below code:
data <- GDCprepare(query, summarizedExperiment = FALSE)
system response me as below:
I think my download process has problem but i don't know what is it?
I appreciate if you share your comment with me.