User: gokce.ouz

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gokce.ouz30
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Singapore
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2 months ago
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Posts by gokce.ouz

<prev • 29 results • page 1 of 3 • next >
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Comment: C: Alternatives to TCGAbiolinks todownload the TCGA Data
... 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 10 weeks ago by gokce.ouz30
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segFault error in getTCGA : 'memory not mapped'
... 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 ...
tcga2stat R brca rna-seq segfault written 10 weeks ago by gokce.ouz30
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Comment: C: Alternatives to TCGAbiolinks todownload the TCGA Data
... 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 weeks ago by gokce.ouz30
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Comment: C: Alternatives to TCGAbiolinks todownload the TCGA Data
... 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 weeks ago by gokce.ouz30
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Comment: C: Error faced for library(TCGAbiolinks)
... Thanks for your reply and clarification. I raised an issue as you suggested. ...
written 10 weeks ago by gokce.ouz30
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Alternatives to TCGAbiolinks todownload the TCGA Data
... 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 ...
tcgabiolinks tcga written 10 weeks ago by gokce.ouz30 • updated 10 weeks ago by vchris_ngs4.2k
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Comment: C: Differential Gene Expression Analysis using data_RNA_Seq_v2_expression_median RS
... Thanks a lot for your answer. ...
written 10 weeks ago by gokce.ouz30
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Error faced for library(TCGAbiolinks)
... 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 ...
tcgabiolinks R tcga written 10 weeks ago by gokce.ouz30 • updated 10 weeks ago by russhh2.7k
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Comment: C: Differential Gene Expression Analysis using data_RNA_Seq_v2_expression_median RS
... 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 11 weeks ago by gokce.ouz30
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Differential Gene Expression Analysis using data_RNA_Seq_v2_expression_median RSEM.Normalized
... 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 ...
R limma rna-seq dge written 11 weeks ago by gokce.ouz30

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Popular Question 9 weeks ago, created a question with more than 1,000 views. For Pre-processing of RNA-Seq data for WGCNA

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