User: Talip Zengin
Talip Zengin • 10
- Reputation:
- 10
- Status:
- New User
- Location:
- Mugla, Turkiye
- Last seen:
- 1 month, 3 weeks ago
- Joined:
- 1 year, 7 months ago
- Email:
- z**********@gmail.com
Posts by Talip Zengin
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... Thanks very much for your quick reply and effort. It is very appreciated :) ...
written 8 weeks ago by
Talip Zengin • 10
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... Hello,
I am using TCGAbiolinks routinely to analyse molecular abnormalities by using heatmap and survival plots. I use the commands below. For 2 days, `TCGAanalyze_survival` has given the error below because *days_to_death* column is missing in expression data downloaded and prepared by `GDCquery`, ...
written 8 weeks ago by
Talip Zengin • 10
• updated
8 weeks ago by
Tiago Chedraoui Silva • 190
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... Hello Sandro, Rina and Martin,
How could you solve this problem? I have same problem, too. ...
written 9 weeks ago by
Talip Zengin • 10
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... Hi. I use gaia package in a linux server to analyze significant CNVs in TCGA samples. During the process load_cnv command takes very very long time and at the end, it gives an error below.
Loading Copy Number Data
............................................................................. ...
written 3 months ago by
Talip Zengin • 10
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... I have tried new version and it works now. Thanks very much for your interest.
...
written 9 months ago by
Talip Zengin • 10
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... Thanks for your interest. I am waiting for new version.
...
written 9 months ago by
Talip Zengin • 10
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... Hi,
I tried again with entrez gene IDs as below, but subnetworks are not generated.
> str(myRankedList)
Named num [1:4412] 4.91e-51 2.76e-49 3.30e-49 2.43e-48 5.59e-48 ...
- attr(*, "names")= chr [1:4412] "177" "857" "6445" "142683" ...
> DEsubs.out <- DEsubs(org='hsa',
+ ...
written 9 months ago by
Talip Zengin • 10
0
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2
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296
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... Hi Panos,
Thanks very much for your reply. I changed my code as you advised, it works now. But the DEsubs.out object does not have subnetworks as result. The structure is as below:
> str(myRankedList)
Named num [1:7292] 5.40e-52 4.91e-51 4.91e-51 3.29e-50 2.76e-49 ...
- attr(*, "names")= chr ...
written 9 months ago by
Talip Zengin • 10
0
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2
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296
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... Hi,
I am using DEsubs for subpathway search for my differentially expressed genes. I get error below when running the DEsubs command. I used this code:
if (.Platform[['OS.type']] == 'unix') {
options('DEsubs_CACHE'=file.path(path.expand("~"), 'DEsubs') ) }
library("DEsubs")
GeneExp_Matrix < ...
written 10 months ago by
Talip Zengin • 10
• updated
9 months ago by
Panos Balomenos • 0
0
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190
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... Hi,
I tried to download maf file for a subset of patients (n=57) through their cases barcodes by using TCGAbiolinks but it downloads all samples (n=565). I tried two different codes below:
library(TCGAbiolinks)
library(SummarizedExperiment)
library(dplyr)
library(DT)
library(maftools)
maf <- ...
written 10 months ago by
Talip Zengin • 10
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