User: gokce.ouz
gokce.ouz • 70
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Posts by gokce.ouz
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C: rsem prepare-reference error
... Hi Amithasandur,
Were you able to solve this problem ? If so, could you share with us ?
Many thanks,
Gokce ...
written 7 months ago by
gokce.ouz • 70
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... Thanks for the suggestions Chris Miller. ...
written 2.6 years ago by
gokce.ouz • 70
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... Hi,
We have specific protein mutations and we are searching for tools to map these protein mutations to the exact location on the genomic DNA.
Do you have any suggestions ?
Thanks ...
written 2.6 years ago by
gokce.ouz • 70
• updated
2.6 years ago by
Chris Miller ♦ 21k
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Comment:
C: Filtering Low Count Genes
... Hi h.mon,
We are trying to find genes that are significantly differentially expressed to identify as signature genes so we need set of genes that show distinct expressional difference between Mutant vs WT.
There is 676 patients in that heatmap:
dim(assay(dds)
[1] 20502 676
This is ho ...
written 2.6 years ago by
gokce.ouz • 70
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C: Filtering Low Count Genes
... Hi Devon,
Thanks for your reply. I tried your suggestion, but I have doubts about my method.
I made the change at the *results()* function as :
res<-results(dds, contrast= c("mutvswt", "Mut", "WT"), filter= rowMedians(counts(dds)))
Is this the correct approach ?
res[order(res$log2Fold ...
written 2.6 years ago by
gokce.ouz • 70
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... Hi All,
I am working on TCGA Breast Cancer dataset. I downloaded the Count data using **TCGA2STAT.**
counts.brca <- getTCGA(disease="BRCA", data.type="RNASeq", type="count")
Extracted the mutation data and clinical data using **library("cgdsr")**
For downstream analysis I am using **DESe ...
written 2.6 years ago by
gokce.ouz • 70
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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 3.0 years ago by
gokce.ouz • 70
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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 3.0 years ago by
gokce.ouz • 70
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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 3.0 years ago by
gokce.ouz • 70
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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 3.0 years ago by
gokce.ouz • 70
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For segFault error in getTCGA : 'memory not mapped'
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For Batch Effect Removal in RNA-Seq Data for DGE & WGCNA. Should I omit any samples according to PCA plots?
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