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User: Talip Zengin

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Talip Zengin10
Reputation:
10
Status:
New User
Location:
Mugla, Turkiye
Last seen:
4 months ago
Joined:
1 year, 3 months 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 5 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 5 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 5 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 5 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 6 months ago by Talip Zengin10 • updated 5 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 6 months 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 6 months 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 6 months ago by Talip Zengin10 • updated 6 months 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 13 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 13 months ago by Talip Zengin10 • updated 13 months ago by Michael Love22k

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