User: Talip Zengin

gravatar for Talip Zengin
Talip Zengin10
Reputation:
10
Status:
New User
Location:
Mugla, Turkiye
Last seen:
3 weeks, 3 days ago
Joined:
11 months, 2 weeks ago
Email:
z**********@gmail.com

Posts by Talip Zengin

<prev • 12 results • page 1 of 2 • next >
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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 24 days 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 6 weeks 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 6 weeks 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 6 weeks 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 7 weeks ago by Talip Zengin10 • updated 6 weeks 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 weeks ago by Talip Zengin10
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Comment: C: Gaia results including negative widths
... Yes, it works now. Thanks very much for your help. ...
written 9 weeks ago by Talip Zengin10
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Gaia results including negative widths
... Hello, I perform CNV analysis by using TCGA data against hg38 and gaia package. After gaia results, at the annotation part, GenomicRanges gives error because of negative widths as below: sCNV_GR <- makeGRangesFromDataFrame(sCNV,keep.extra.columns = TRUE) Error in .Call2("solve_user_SEW0", start ...
iranges genomicranges gaia written 9 weeks ago by Talip Zengin10 • updated 9 weeks ago by Sandro Morganella30
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Comment: C: DESeq2 - Design for TCGA unpaired RNAseq data
... Thank so very much for your advices. ...
written 9 months ago by Talip Zengin10
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DESeq2 - Design for TCGA unpaired RNAseq data
... Hello everybody, I am using TCGA LUAD RNAseq data for DEG analysis. There are data of 522 patients, only 59 of them have paired (have normal and tumor sample) data without replicates. Can I compare all data of tumor samples (522) against all data of normal samples (59)? Is it possible in statistics ...
rnaseq deseq2 unpaired design tcga written 9 months ago by Talip Zengin10 • updated 9 months ago by Michael Love19k

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