User: Talip Zengin

gravatar for Talip Zengin
Talip Zengin • 10
Reputation:
10
Status:
New User
Location:
Mugla, Turkiye
Last seen:
1 month, 2 weeks ago
Joined:
1 year, 11 months ago
Email:
z**********@gmail.com

Posts by Talip Zengin

<prev • 19 results • page 1 of 2 • next >
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Which one is more trustable for Cox Proportional Hazard Model with Lasso penalty? LOOCV or K-fold cross-validation?
... Hi, When I checked articles to find a method to identify predictors of overall survival, mostly glmnet cox model is used with Lasso penalty and cross validation. As cross validation, people used 10-fold cross validation with 1000 iterations or LOOCV. I read about glmnet method and searched forums f ...
glmnet cox loocv k-fold cross validation written 6 weeks ago by Talip Zengin • 10 • updated 6 weeks ago by chris86 • 380
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Comment: C: TCGAbiolinks GDCprepare error
... Thanks very much for your reply. I updated with github version and now it works. ...
written 3 months ago by Talip Zengin • 10
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TCGAbiolinks GDCprepare error
... Hi, I am using TCGAbiolinks package for my pipeline. Today I got the error below. Could you please help me on fixing this error? GeneExp_paired <- GDCprepare(query_exp, save = TRUE, save.filename = paste0(cancer, "_GeneExp_paired.rda")) |========================================= ...
error tcgabiolinks gdcprepare written 3 months ago by Talip Zengin • 10 • updated 3 months ago by tiagochst • 150
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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 5 months ago by Talip Zengin • 10
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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 5 months ago by Talip Zengin • 10 • updated 5 months ago by Tiago Chedraoui Silva • 240
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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 6 months ago by Talip Zengin • 10
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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 7 months ago by Talip Zengin • 10
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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 12 months ago by Talip Zengin • 10
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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 13 months ago by Talip Zengin • 10
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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 13 months ago by Talip Zengin • 10

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