Tag: ConsensusClusterPlus
A Novel Model Using Ferroptosis-Related Genes Predicts Prognosis in DLBCLs
The following is a summary of “Identification of a novel model based on ferroptosis-related genes for predicting the prognosis of diffuse large B-cell lymphomas,” published in the May 2023 issue of Hematology by Wang, et al. Diffuse large B-cell lymphomas (DLBCLs) are characterized by their phenotypic and genetic heterogeneity. For…
IL5RA as an immunogenic cell death-related predictor in progression and therapeutic response of multiple myeloma
Differential expression analysis We downloaded GSE125361 (n = 48) microarray data from the Gene Expression Omnibus (GEO) database, which included 45 myeloma samples and 3 controls, for expression analysis of IL5RA in cancer16. Additionally, we analyzed the expression of IL5RA in smoldering myeloma (SMM) patients who progressed to active MM (n = 10) and…
An integrated tumor, immune and microbiome atlas of colon cancer
Samples used in this observational cohort study (tumor tissue and matched healthy colon tissue, AC-ICAM cohort) are from patients with colon cancer diagnosed at Leiden University Medical Center, the Netherlands, from 2001 to 2015 that did not object for future use of human tissues for scientific research and that were…
Nidogen-2 (NID2) is a Key Factor in Collagen Causing Poor Response to
Yan Sha,1,* An-qi Mao,1,* Yuan-jie Liu,2 Jie-pin Li,2 Ya-ting Gong,3 Dong Xiao,1 Jun Huang,1 Yan-wei Gao,1 Mu-yao Wu,3 Hui Shen1 1Departments of Dermatology, Zhangjiagang TCM Hospital Affiliated to Nanjing University of Chinese Medicine, Zhangjiagang, People’s Republic of China; 2Department of Oncology, Affiliated Hospital of Nanjing University of Chinese Medicine, Jiangsu…
Identification and validation of BCL6 and VEGFA as biomarkers and ageing patterns correlating with immune infiltrates in OA progression
Hunter, D. J. & Bierma-Zeinstra, S. Osteoarthritis. Lancet 393, 1745–1759 (2019). Article CAS Google Scholar Hunter, D. J., March, L. & Chew, M. Osteoarthritis in 2020 and beyond: A Lancet Commission. Lancet 396, 1711–1712 (2020). Article Google Scholar Puig-Junoy, J. & RuizZamora, A. Socio-economic costs of osteoarthritis: A systematic review…
Immune Infiltration and N(6)-Methyladenosine ncRNA Isoform Detection in Acute Lung Injury
Acute lung injury (ALI) is a severe form of sepsis that is associated with a high rate of morbidity and death in critically ill individuals. The emergence of ALI is the result of several factors at work. Case mortality rates might range from 40% to 70%. Researchers have discovered that…
ConsensusClusterPlus package
ConsensusClusterPlus package 0 Hi guys, How can I check the plots individually, when I run the ConsensusClusterPlus command they are generated above each other very fast and end up with Tracking plot, I cant find them anywhere else, I tried to generate them as PDFs or as png but nothing…
How to extract most contributing features for each cluster
ConsensusClusterPlus: How to extract most contributing features for each cluster 0 Hi, I am using the R package ConsensusClusterPlus. Here is an example with the ALL data: library(ConsensusClusterPlus) library(ALL) data(ALL) d = exprs(ALL) res <- ConsensusClusterPlus(d, clusterAlg = “pam”, finalLinkage = “average”, distance = “spearman”, plot = NULL, reps =…
How to extract plots from ConsensusClusterPlus package
Hello All, Is there a way to extract the plots separately from the ConsensusClusterPlus package? For example, using the example data from the package, I can print the last three plots as below, library(ALL) data(ALL) d=exprs(ALL) mads=apply(d,1,mad) d=d[rev(order(mads))[1:5000],] d = sweep(d,1, apply(d,1,median,na.rm=T)) library(ConsensusClusterPlus) par(mfrow=c(1,3)) title=tempdir() results = ConsensusClusterPlus(d,maxK=6,reps=50,pItem=0.8,pFeature=1, title=title,clusterAlg=”hc”,distance=”pearson”,seed=1262118388.71279) But,…
