Tag: GISTIC

My goal is to produce an OncoPlot with somatic mutation, copy number, and clinical information. I’m able to produce a MAF file with clinical info: maf.plus.clin <- read.maf( maf = maf, clinicalData = clinical.all, ) and also a MAF file with GISTIC info: maf.plus.gistic <- read.maf( maf = maf, gisticAllLesionsFile…

I am pretty new to GISTIC plots. I am making a plot for my WES sample. I have made marker file based on id, chrom and marker positions. After uploading my SEG and marker file, I got an error. GISTIC version 2.0.23 Warning: Number of markers is less than smooth…

Hello, Shahin here.I am very happy that such a group exists.other than that, just want to thank you to make open source GenePattern, which saves us lots of work and saves lots of time. I am new to Gene analysis and because of that, trying to do a sample project.For…

absolute running error: Error in if (!is.na(res)) { : the condition has length > 1 0 the following are my R codes: install.packages(“numDeriv”) BiocManager::install(“DNAcopy”) install.packages(“ABSOLUTE_1.0.6.tar.gz”,repos = NULL) library(numDeriv) library(ABSOLUTE) RunAbsolute( seg.dat.fn = “P01_1_GISTIC_segment”, sigma.p = 0, max.sigma.h = 0.2, min.ploidy = 0.5, max.ploidy = 8, primary.disease = “NPC”, platform =…

B cells undergo a series of programmed genomic alterations that enable the immunoglobulin light and heavy chain loci to generate high-affinity antibodies against invading pathogens. First, B cells undergo variability, diversity and joining (VDJ) recombination in the bone marrow with subsequent somatic hypermutation (SHM) and class switch recombination (CSR) occurring…

Conumee output as input for Gistic2.0 0 Hi Biostars! I am currently undertaking a CNA-analysis, in which i have access to methylation array data (Infinium EPIC). After generating CNV data through conumee, i would like to use this output for further processing using Gistic 2 to study CNAs at a…

How to use conumee segment mean for gistic input 0 I have segment mean from methylation EPIC array ( when performing copy number analysis using conumee package) and want to use this with gistic tool which required “Seg.CN (log2() -1 of copy number)” column in the main input. Someone explained…

TCGA/Broad Institute CNV Files Segment Mean 3 Hello everybody, I am trying to analyse CNV data from TCGA to get a measure of overall CNV per patient. When I download the Level 3 files taken from the SNP6 array, there is a column in the file called Segment_Mean. (Example at…

GISTIC isn’t checking chromosome 23 / X 0 Hi, I have a problem with GISTIC apparently not checking for CNV on chromosome X. GISTIC2 runs without errors on my segmentation file with the supplied reference file refgenefile=refgenefiles/hg38.UCSC.add_miR.160920.refgene.mat My input file has CNV events in chromosome ’23’ but the GISTIC run…

Hello, I ran my analysis on GISTIC_2.0 version 6.15.30 on Gene Pattern. I have 58 samples of whole genome sequencing data with the seg copy number file. I prepared the input for gistic as stated in the literature and the forum: a txt file with 6 columns: sample, chromosome, start,…

Understanding consensus CNV of PCAWG data 0 Hi everyone, I want to get the exact copy number of each gene for each sample in PCAWG I have located this PCAWG directory dcc.icgc.org/releases/PCAWG/consensus_cnv/gene_level_calls However, there are three files listed there: all_samples.consensus_CN.by_gene.170214.txt.gz all_samples.consensus_CN.minor_allele.by_gene.170313.txt.gz all_samples.consensus_level_calls.by_gene.170214.txt.gz I cannot find any description of these files…

GISTIC2 Index exceeds matrix dimensions. 0 I encountered the following issues while using GISTIC2 online analysis. How can I solve them? Index exceeds matrix dimensions. Error in normalize_by_arm_length (line 85) Error in make_sample_B (line 50) Error in perform_deconstruction (line 68) Error in perform_ziggurat_deconstruction (line 126) Error in run_focal_gistic (line 151)…

The National Institute of Deafness and Other Communication Disorders, Bethesda, Maryland Position Description: The Division of Intramural Research (DIR), National Institute on Deafness and Other Communication Disorders (NIDCD), National Institutes of Health (NIH), Department of Health and Human Services (DHHS) seeks a Staff Scientist. The NIDCD intramural program comprises a highly…

GISTIC from ASCAT 0 Hello everyone, I am trying to run GISTIC from ASCAT segments, however,i am running into the following error. 1935 segment overlaps detected I read somewhere that running bedtools merge would solve the problem, however I am not sure. Is anyone doing the same ? or adopting…

Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK Christopher Abbosh, Alexander M. Frankell, Selvaraju Veeriah, Sophia Ward, Kristiana Grigoriadis, Kevin Litchfield, Clare Puttick, Dhruva Biswas, Takahiro Karasaki, James R. M. Black, Carlos Martínez-Ruiz, Maise Al Bakir, Emilia L. Lim, Ariana Huebner, David A. Moore, Elizabeth Manzano, Crispin T. Hiley, Mariam Jamal-Hanjani, Abigail Bunkum, Antonia Toncheva, Corentin Richard, Cristina Naceur-Lombardelli, Foteini Athanasopoulou, Francisco Gimeno-Valiente, Haoran Zhai, Jie Min Lam, Kerstin…

The TRACERx 421 cohort The TRACERx study (clinicaltrials.gov/ct2/show/NCT01888601) is a prospective observational cohort study that aims to transform our understanding of NSCLC, the design of which has been approved by an independent research ethics committee (13/LO/1546). Informed consent for entry into the TRACERx study was mandatory and obtained from every…

CNA plots with gene names using GISTIC 0 I have the GISTIC plots with amplification and deletion for my data but the plots show chromosome region where as I want to have gene names on the peak positions. I have attach a demo diagram below. visualization CNA GISTIC • 72…

Gaia CNV error TCGA data 0 Dear All, I am trying to analyze some TCGA CNV data using the GAIA package. I followed the tutorial from @kevinblighe. Everything runs well and at the end, the error below come up. Has someone witnessed this before anc could some one propose a…

Interpreting ASCAT CNV output 1 Hello, I have two queries w.r.t ASCAT CNV data: How does one go about getting the total copy number for a given locus or chromosome from the ASCAT CNV.output results. What is the optimal way to filter the dataset to reduce the noise? I would…

This article was originally published here BMC Med Genomics. 2022 Jan 3;15(1):1. doi: 10.1186/s12920-021-01143-2. ABSTRACT BACKGROUND: Renal collecting duct carcinoma (CDC) is a rare and lethal subtype of renal cell carcinoma (RCC). The genomic profile of the Chinese population with CDC remains unclear. In addition, clinical treatments are contradictory. In…

Copy number differences between groups 0 Analogous to differential expression with RNA data, is there a statistic or tool to analyze the frequency of copy number alterations between two groups? I had imagined this to be a Chi-square performed like 20,000 times (each gene) to see if that particular gene…