User: Talip Zengin

gravatar for Talip Zengin
Talip Zengin10
Reputation:
10
Status:
New User
Location:
Mugla, Turkiye
Last seen:
1 day, 17 hours ago
Joined:
1 year, 5 months ago
Email:
z**********@gmail.com

Posts by Talip Zengin

<prev • 16 results • page 1 of 2 • next >
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Comment: C: Missing clinical data at TCGAbiolinks data
... Thanks very much for your quick reply and effort. It is very appreciated :) ...
written 1 day ago by Talip Zengin10
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Missing clinical data at TCGAbiolinks data
... 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`, ...
tcgabiolinks days_to_death clinical data missing column written 6 days ago by Talip Zengin10 • updated 5 days ago by Tiago Chedraoui Silva190
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Comment: C: Gaia not returning results - load_cnv problem
... Hello Sandro, Rina and Martin, How could you solve this problem? I have same problem, too. ...
written 12 days ago by Talip Zengin10
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Gaia Package Load CNV Error
... 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 ............................................................................. ...
gaia load_cnv written 6 weeks ago by Talip Zengin10
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Comment: C: DEsubs - Error in read.table during DEsubs command
... I have tried new version and it works now. Thanks very much for your interest. ...
written 7 months ago by Talip Zengin10
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Comment: C: DEsubs - Error in read.table during DEsubs command
... Thanks for your interest. I am waiting for new version. ...
written 7 months ago by Talip Zengin10
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Comment: C: DEsubs - Error in read.table during DEsubs command
... 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 7 months ago by Talip Zengin10
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Comment: C: DEsubs - Error in read.table during DEsubs command
... 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 7 months ago by Talip Zengin10
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DEsubs - Error in read.table during DEsubs command
... 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 < ...
error desubs written 8 months ago by Talip Zengin10 • updated 7 months ago by Panos Balomenos0
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How to download TCGA mutation data by TCGAbiolinks for a subset of barcode?
... 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 <- ...
tcgabiolinks written 8 months ago by Talip Zengin10

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