scholarly journals A Simple Rank Product Approach for Analyzing Two Classes

2015 ◽  
Vol 9 ◽  
pp. BBI.S26414 ◽  
Author(s):  
Tae Young Yang

The rank product statistic has been widely used to detect differentially expressed genes in replicated microarrays and a one-class setting. The objective of this article is to apply a rank product statistic to approximate the P-value of differential expression in a two-class setting, such as in normal and cancer cells. For this purpose, we introduce a simple statistic that compares the P-values of each class's rank product statistic. Its null distribution is straightforwardly derived using the change-of-variable technique.

2016 ◽  
Author(s):  
Mamoun Ahram ◽  
Rand Zaza ◽  
Ebtihal Mustafa ◽  
Heba Jarrar ◽  
Razan Al-Saber ◽  
...  

2020 ◽  
Vol 79 (Suppl 1) ◽  
pp. 1048.2-1048
Author(s):  
S. Herrera ◽  
J. C. Diaz-Coronado ◽  
D. Rojas-Gualdrón ◽  
L. Betancur-Vasquez ◽  
D. Gonzalez-Hurtado ◽  
...  

Background:Systemic lupus erythematosus (SLE) clinical manifestations, and their severity, vary according to age, ethnicity and socioeconomic status. Both Hispanic and Afro-Americans have a higher incidence and more sever presentation when compared to Caucasian patients with SLEObjectives:To analyze clinical and immunological characteristics associated with time to severe renal involvement in patients with Systemic Lupus Erythematous in a Colombian cohort followed for one year, between January 2015 and December 2018Methods:Retrospective follow-up study based in clinical records. Patients with SLE diagnosis that fulfilled either 1987 American College of Rheumatology Classification Criteria for SLE or 2011 Systemic Lupus International Collaborating Clinics (SLICC) classification criteria for SLE. We included patients with diagnosis of lupus nephritis according to Wallace and Dubois criteria. Patients who did not have at least two follow-up measurements or had a cause of nephritis other than lupus were excluded. The main outcome was defined as time from diagnosis to sever renal involvement defined as creatinine clearance ≤50 ml/min, 24-hour proteinuria ≥3.5 grams o end stage renal disease.We analyzed clinical and immunological characteristics. Descriptive statistical analyses of participant data during the first evaluation are reported as frequencies and percentages for categorical variables, and as medians and interquartile ranges (IQR) for quantitative variables. Age and sex adjusted survival functions and Hazard ratios (HR) with 95% confidence intervals and p-values were estimated using parametric Weibull models por interval-censored data. P values < 0.05 were considered statistically significantResults:548 patients were analyzed: 67 were left-censored as they presented renal involvement at entry, 6 were interval censored as outcome occurred between study visits, and 475 were right-censored as involvement was not registered during follow-up. 529 (96.5%) patients were female, median age at entry was 46 (IQR = 23) and median age to diagnosis was 29.5 (IQR = 20.6). 67% were mestizo, 13% Caucasian and 0.3% Afro-Colombian. Age and sex adjusted variables associated with time to severe lupus nephritis were high blood pressure HR = 3.5 (95%CI 2.2-5.6; p-value <0.001) and Anti-RO (per unit increase) HR = 1.002 (95%CI 1.001-1.004; p-value = 0.04). Figure 1 shows age and sex adjusted survival function.Conclusion:In our cohort the appearance of severe lupus nephritis occurs in less than 15% of patients at 10 years. Both high blood pressure and elevated anti-Ro titers were associated with a higher rate of onset in the presentation of severe lupus nephritis, as seen in some polymorphs of anti Ro.References:Disclosure of Interests:Sebastian Herrera Speakers bureau: academic conference, Juan camilo Diaz-Coronado: None declared, Diego Rojas-Gualdrón: None declared, Laura Betancur-Vasquez: None declared, Daniel Gonzalez-Hurtado: None declared, Juanita Gonzalez-Arango: None declared, laura Uribe-Arango: None declared, Maria Fernanda Saavedra Chacón: None declared, Jorge Lacouture-Fierro: None declared, Santiago Monsalve: None declared, Sebastian Guerra-Zarama: None declared, Juan david Lopez: None declared, Juan david Serna: None declared, Julian Barbosa: None declared, Ana Sierra: None declared, Deicy Hernandez-Parra: None declared, Ricardo Pineda.Tamayo: None declared


2007 ◽  
Vol 3 ◽  
pp. 117693510700300
Author(s):  
Yingye Zheng ◽  
Margaret Pepe

Consider a gene expression array study comparing two groups of subjects where the goal is to explore a large number of genes in order to select for further investigation a subset that appear to be differently expressed. There has been much statistical research into the development of formal methods for designating genes as differentially expressed. These procedures control error rates such as the false detection rate or family wise error rate. We contend however that other statistical considerations are also relevant to the task of gene selection. These include the extent of differential expression and the strength of evidence for differential expression at a gene. Using real and simulated data we first demonstrate that a proper exploratory analysis should evaluate these aspects as well as decision rules that control error rates. We propose a new measure called the mp-value that quantifies strength of evidence for differential expression. The mp-values are calculated with a resampling based algorithm taking into account the multiplicity and dependence encountered in microarray data. In contrast to traditional p-values our mp-values do not depend on specification of a decision rule for their definition. They are simply descriptive in nature. We contrast the mp-values with multiple testing p-values in the context of data from a breast cancer prognosis study and from a simulation model.


PEDIATRICS ◽  
1996 ◽  
Vol 98 (6) ◽  
pp. A22-A22
Author(s):  
Student

When we are told that "there's no evidence that A causes B," we should first ask whether absence of evidence means simply that there is no information at all. If there are data, we should look for quantification of the association rather than just a P value. Where risks are small, P values may well mislead: confidence intervals are likely to be wide, indicating considerable uncertainty.


Stroke ◽  
2021 ◽  
Vol 52 (Suppl_1) ◽  
Author(s):  
Sarah E Wetzel-Strong ◽  
Shantel M Weinsheimer ◽  
Jeffrey Nelson ◽  
Ludmila Pawlikowska ◽  
Dewi Clark ◽  
...  

Objective: Circulating plasma protein profiling may aid in the identification of cerebrovascular disease signatures. This study aimed to identify circulating angiogenic and inflammatory biomarkers that may serve as biomarkers to differentiate sporadic brain arteriovenous malformation (bAVM) patients from other conditions with brain AVMs, including hereditary hemorrhagic telangiectasia (HHT) patients. Methods: The Quantibody Human Angiogenesis Array 1000 (Raybiotech) is an ELISA multiplex panel that was used to assess the levels of 60 proteins related to angiogenesis and inflammation in heparin plasma samples from 13 sporadic unruptured bAVM patients (69% male, mean age 51 years) and 37 patients with HHT (40% male, mean age 47 years, n=19 (51%) with bAVM). The Quantibody Q-Analyzer tool was used to calculate biomarker concentrations based on the standard curve for each marker and log-transformed marker levels were evaluated for associations between disease states using a multivariable interval regression model adjusted for age, sex, ethnicity and collection site. Statistical significance was based on Bonferroni correction for multiple testing of 60 biomarkers (P< 8.3x10 - 4 ). Results: Circulating levels of two plasma proteins differed significantly between sporadic bAVM and HHT patients: PDGF-BB (P=2.6x10 -4 , PI= 3.37, 95% CI:1.76-6.46) and CCL5 (P=6.0x10 -6 , PI=3.50, 95% CI=2.04-6.03). When considering markers with a nominal p-value of less than 0.01, MMP1 and angiostatin levels also differed between patients with sporadic bAVM and HHT. Markers with nominal p-values less than 0.05 when comparing sporadic brain AVM and HHT patients also included angiostatin, IL2, VEGF, GRO, CXCL16, ITAC, and TGFB3. Among HHT patients, the circulating levels of UPAR and IL6 were elevated in patients with documented bAVMs when considering markers with nominal p-values less than 0.05. Conclusions: This study identified differential expression of two promising plasma biomarkers that differentiate sporadic bAVMs from patients with HHT. Furthermore, this study allowed us to evaluate markers that are associated with the presence of bAVMs in HHT patients, which may offer insight into mechanisms underlying bAVM pathophysiology.


2018 ◽  
Vol 12 (5) ◽  
pp. 456-462 ◽  
Author(s):  
Zhipeng Sun ◽  
Yubing Zhu ◽  
Aminbuhe ◽  
Qing Fan ◽  
Jirun Peng ◽  
...  

Econometrics ◽  
2019 ◽  
Vol 7 (1) ◽  
pp. 11 ◽  
Author(s):  
Richard Startz

As a contribution toward the ongoing discussion about the use and mis-use of p-values, numerical examples are presented demonstrating that a p-value can, as a practical matter, give you a really different answer than the one that you want.


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