User: gokce.ouz
gokce.ouz • 30
- Reputation:
- 30
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- Location:
- Singapore
- Last seen:
- 5 days, 2 hours ago
- Joined:
- 2 years, 11 months ago
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Posts by gokce.ouz
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... Hi vchris_ngs,
I checked the TCGA2STAT. As you said it is what I need,thanks a lot! However, I guess the luck is not on my side, because now, I am getting segfault errors which I posted [here][1] to ask for help.
[1]: https://www.biostars.org/p/272544/ ...
written 9 days ago by
gokce.ouz • 30
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... Hi All,
I wanted to use TCGA2STAT package to download Breast cancer data. However, I am facing the segfault error. I posted an issue on their github page. But they did not reply back to another user who raised the same issue last January. Therefore, could you please help me solve this problem?
Tha ...
written 9 days ago by
gokce.ouz • 30
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... sessionInfo()
R version 3.4.1 (2017-06-30)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS release 6.5 (Final)
Matrix products: default
BLAS: /mnt/software/stow/R-3.4.1/lib64/R/lib/libRblas.so
LAPACK: /mnt/software/stow/R-3.4.1/lib64/R/lib/libRlapack.so
...
written 10 days ago by
gokce.ouz • 30
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... Thanks a lot for your reply. I will check the alternative you suggested. Also I posted the issue at github, but saw that another user also raised it 8 days ago. Hopefully, they will fix the issue soon.
The error occurs when I want to use the library. The installations of R packages are done by syste ...
written 10 days ago by
gokce.ouz • 30
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... Thanks for your reply and clarification. I raised an issue as you suggested.
...
written 10 days ago by
gokce.ouz • 30
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... Hi All,
**library(TCGAbiolinks)** is giving errors as *gridExtra* was renamed so I can not use it to download and analyzing the TCGA data. Except **GDC Portal** (our IT support having problems to install the data transfer tool, so I can not use it right now) is there any other alternatives to get t ...
written 10 days ago by
gokce.ouz • 30
• updated
10 days ago by
vchris_ngs • 4.0k
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... Thanks a lot for your answer.
...
written 10 days ago by
gokce.ouz • 30
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... Hi,
I am working on server. Whenever I want to use **library(TCGAbiolinks)** I am facing the error below. How could I solve this problem ?
Thanks in advance,
Gokce
> Error: package or namespace load failed for âTCGAbiolinksâ: object
> ârbind.gtableâ is not exported by 'namespace:gridExtr ...
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... Dear Kristoffer,
Thanks a lot for your answer.
I knew I would be more comfortable with the raw data however I was being forced to work on this normalized data. Maybe it is better to insist on working on the raw data again.
So to clarify, you are suggesting me to use voom+limma on the raw count da ...
written 18 days ago by
gokce.ouz • 30
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... Hi All,
We have a specific gene mutation and we would like to learn how it is effective on Breast cancer.
So using the R, I get the mutation information from sequenced cases of TCGA Provisional and then stratified patients into two categories as Mutated & Wild Type. I downloaded the mRNA Expr ...
written 18 days ago by
gokce.ouz • 30
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